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Ramírez-Bello I, López T, Espinosa R, Ghosh A, Green K, Riaño-Umbarila L, Gaspar-Castillo C, Alpuche-Aranda CM, López S, DuBois RM, Arias CF. Antigenic determinants of HAstV-VA1 neutralization and their relevance in the human immune response. bioRxiv 2024:2024.03.05.583477. [PMID: 38496431 PMCID: PMC10942293 DOI: 10.1101/2024.03.05.583477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Astroviruses are highly divergent and infect a wide variety of animal hosts. In 2009, a genetically divergent human astrovirus (HAstV) strain VA1 was first identified in an outbreak of acute gastroenteritis. This strain has also been associated with fatal central nervous system disease. In this work, we report the isolation of three high-affinity neutralizing monoclonal antibodies (Nt-MAbs) targeting the capsid spike domain of HAstV-VA1. These antibodies (7C8, 2A2, 3D8) were used to select individual HAstV-VA1 mutants resistant to their neutralizing activity and also select a HAstV-VA1 triple mutant that escapes neutralization from all three Nt-MAbs. Sequencing of the virus genome capsid region revealed escape mutations that map to the surface of the capsid spike domain, define three potentially independent neutralization epitopes, and help delineate four antigenic sites in rotaviruses. Notably, two of the escape mutations were found to be present in the spike sequence of the HAstV-VA1-PS strain isolated from an immunodeficient patient with encephalitis, suggesting that those mutations arose as a result of the immune pressure generated by the patient's immunotherapy. In accordance with this observation, human serum samples exhibiting strong neutralization activity against wild-type HAstV-VA1 had a 2.6-fold reduction in neutralization titer when evaluated against the triple-escape HAstV-VA1 mutant, indicating shared neutralization epitopes between the mouse and human antibody response. The isolated Nt-MAbs reported in this work will help characterize the functional sites of the virus during cell entry and have the potential for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1. Importance Human astroviruses (HAstVs) have been historically associated with acute gastroenteritis. However, the genetically divergent HAstV-VA1 strain has been associated with central nervous system disease. This work isolated high-affinity neutralizing monoclonal antibodies directed to HAstV-VA1. The proposed binding sites for these antibodies, together with previously reported sites for neutralizing antibodies against classical HAstVs, suggest the existence of at least four neutralization sites on the capsid spike of astroviruses. Our data show that natural infection with human astrovirus VA1 elicits a robust humoral immune response that targets the same antigenic sites recognized by the mouse monoclonal antibodies and strongly suggests the emergence of a variant HAstV-VA1 virus in an immunodeficient patient with prolonged astrovirus infection. The isolated Nt-MAb reported in this work will be helpful in defining the functional sites of the virus involved in cell entry and hold promise for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1.
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García-López R, Taboada B, Zárate S, Muñoz-Medina JE, Salas-Lais AG, Herrera-Estrella A, Boukadida C, Vazquez-Perez JA, Gómez-Gil B, Sanchez-Flores A, Arias CF. Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover. Microb Genom 2024; 10:001220. [PMID: 38512312 PMCID: PMC11004493 DOI: 10.1099/mgen.0.001220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Sinaloa, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Hernández-Guzmán J, Arias CF, López S, Sandoval-Jaime C. Nucleolin-RNA interaction modulates rotavirus replication. J Virol 2024; 98:e0167723. [PMID: 38240590 PMCID: PMC10878083 DOI: 10.1128/jvi.01677-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 02/21/2024] Open
Abstract
Rotavirus infection is a leading cause of gastroenteritis in children worldwide; the genome of this virus is composed of 11 segments of dsRNA packed in a triple-layered protein capsid. Here, we investigated the role of nucleolin, a protein with diverse RNA-binding domains, in rotavirus infection. Knocking down the expression of nucleolin in MA104 cells by RNA interference resulted in a remarkable 6.3-fold increase in the production of infectious rhesus rotavirus (RRV) progeny, accompanied by an elevated synthesis of viral mRNA and genome copies. Further analysis unveiled an interaction between rotavirus segment 10 (S10) and nucleolin, potentially mediated by G-quadruplex domains on the viral genome. To determine whether the nucleolin-RNA interaction regulates RRV replication, MA104 cells were transfected with AGRO100, a compound that forms G4 structures and selectively inhibits nucleolin-RNA interactions by blocking the RNA-binding domains. Under these conditions, viral production increased by 1.5-fold, indicating the inhibitory role of nucleolin on the yield of infectious viral particles. Furthermore, G4 sequences were identified in all 11 RRV dsRNA segments, and transfection of oligonucleotides representing G4 sequences in RRV S10 induced a significant increase in viral production. These findings show that rotavirus replication is negatively regulated by nucleolin through the direct interaction with the viral RNAs by sequences forming G4 structures.IMPORTANCEViruses rely on cellular proteins to carry out their replicative cycle. In the case of rotavirus, the involvement of cellular RNA-binding proteins during the replicative cycle is a poorly studied field. In this work, we demonstrate for the first time the interaction between nucleolin and viral RNA of rotavirus RRV. Nucleolin is a cellular protein that has a role in the metabolism of ribosomal rRNA and ribosome biogenesis, which seems to have regulatory effects on the quantity of viral particles and viral RNA copies of rotavirus RRV. Our study adds a new component to the current model of rotavirus replication, where cellular proteins can have a negative regulation on rotavirus replication.
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Affiliation(s)
- Jey Hernández-Guzmán
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos Sandoval-Jaime
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Garay E, Whelan SPJ, DuBois RM, O’Rourke SM, Salgado-Escobar AE, Muñoz-Medina JE, Arias CF, López S. Immune response to SARS-CoV-2 variants after immunization with different vaccines in Mexico. Epidemiol Infect 2024; 152:e30. [PMID: 38312015 PMCID: PMC10894899 DOI: 10.1017/s0950268824000219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/11/2024] [Accepted: 01/24/2024] [Indexed: 02/06/2024] Open
Abstract
There is limited information on the antibody responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in subjects from developing countries with populations having a high incidence of co-morbidities. Here, we analysed the immunogenicity of homologous schemes using the ChAdOx1-S, Sputnik V, or BNT162b2 vaccines and the effect of a booster dose with ChAdOx1-S in middle-aged adults who were seropositive or seronegative to the SARS-CoV-2 spike protein before vaccination. The study was conducted post-vaccination with a follow-up of 4 months for antibody titre using enzyme-linked immunosorbent assay (ELISA) and pseudovirus (PV) neutralization assays (PNAs). All three vaccines elicited a superior IgG anti-receptor-binding domain (RBD) and neutralization response against the Alpha and Delta variants when administered to individuals with a previous infection by SARS-CoV-2. The booster dose spiked the neutralization activity among individuals with and without a prior SARS-CoV-2 infection. The ChAdOx1-S vaccine induced weaker antibody responses in infection-naive subjects. A follow-up of 4 months post-vaccination showed a drop in antibody titre, with about 20% of the infection-naive and 100% of SARS-CoV-2 pre-exposed participants with detectable neutralization capacity against Alpha pseudovirus (Alpha-PV) and Delta PV (Delta-PV). Our observations support the use of different vaccines in a country with high seroprevalence at the vaccination time.
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Affiliation(s)
- Erika Garay
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University in St. Louis, Saint Louis, United States
- Department of Microbiology, Harvard Medical School, Boston, United States
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California, Santa Cruz, United States
| | - Sara M. O’Rourke
- Department of Biomolecular Engineering, University of California, Santa Cruz, United States
| | - Angel Eduardo Salgado-Escobar
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Ghosh A, Delgado-Cunningham K, López T, Green K, Arias CF, DuBois RM. Structure and antigenicity of the divergent human astrovirus VA1 capsid spike. PLoS Pathog 2024; 20:e1012028. [PMID: 38416796 PMCID: PMC10950212 DOI: 10.1371/journal.ppat.1012028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/19/2024] [Accepted: 02/05/2024] [Indexed: 03/01/2024] Open
Abstract
Human astrovirus (HAstV) is a known cause of viral gastroenteritis in children worldwide, but HAstV can cause also severe and systemic infections in immunocompromised patients. There are three clades of HAstV: classical, MLB, and VA/HMO. While all three clades are found in gastrointestinal samples, HAstV-VA/HMO is the main clade associated with meningitis and encephalitis in immunocompromised patients. To understand how the HAstV-VA/HMO can infect the central nervous system, we investigated its sequence-divergent capsid spike, which functions in cell attachment and may influence viral tropism. Here we report the high-resolution crystal structures of the HAstV-VA1 capsid spike from strains isolated from patients with gastrointestinal and neuronal disease. The HAstV-VA1 spike forms a dimer and shares a core beta-barrel structure with other astrovirus capsid spikes but is otherwise strikingly different, suggesting that HAstV-VA1 may utilize a different cell receptor, and an infection competition assay supports this hypothesis. Furthermore, by mapping the capsid protease cleavage site onto the structure, the maturation and assembly of the HAstV-VA1 capsid is revealed. Finally, comparison of gastrointestinal and neuronal HAstV-VA1 sequences, structures, and antigenicity suggests that neuronal HAstV-VA1 strains may have acquired immune escape mutations. Overall, our studies on the HAstV-VA1 capsid spike lay a foundation to further investigate the biology of HAstV-VA/HMO and to develop vaccines and therapeutics targeting it.
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Affiliation(s)
- Anisa Ghosh
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kevin Delgado-Cunningham
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Kassidy Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
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Pirani RM, Arias CF, Charles K, Chung AK, Curlis JD, Nicholson DJ, Vargas M, Cox CL, McMillan WO, Logan ML. A high-quality genome for the slender anole (Anolis apletophallus): an emerging model for field studies of tropical ecology and evolution. G3 (Bethesda) 2023; 14:jkad248. [PMID: 37875105 PMCID: PMC10755174 DOI: 10.1093/g3journal/jkad248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 01/22/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023]
Abstract
The slender anole, Anolis apletophallus, is a small arboreal lizard of the rainforest understory of central and eastern Panama. This species has been the subject of numerous ecological and evolutionary studies over the past 60 years as a result of attributes that make it especially amenable to field and laboratory science. Slender anoles are highly abundant, short-lived (nearly 100% annual turnover), easy to manipulate in both the lab and field, and are ubiquitous in the forests surrounding the Smithsonian Tropical Research Institute in Panama, where researchers have access to high-quality laboratory facilities. Here, we present a high-quality genome for the slender anole, which is an important new resource for studying this model species. We assembled and annotated the slender anole genome by combining 3 technologies: Oxford Nanopore, 10× Genomics Linked-Reads, and Dovetail Omni-C. We compared this genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. Our genome is the first assembled for an Anolis lizard from mainland Central or South America, the regions that host the majority of diversity in the genus. This new reference genome is one of the most complete genomes of any anole assembled to date and should facilitate deeper studies of slender anole evolution, as well as broader scale comparative genomic studies of both mainland and island species. In turn, such studies will further our understanding of the well-known adaptive radiation of Anolis lizards.
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Affiliation(s)
- Renata M Pirani
- Department of Biology, University of Nevada Reno, Reno, NV 89557, USA
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Carlos F Arias
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20013, USA
| | - Kristin Charles
- Department of Biology, University of Nevada Reno, Reno, NV 89557, USA
| | - Albert K Chung
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-2016, USA
| | - John David Curlis
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI 48109-1085, USA
| | - Daniel J Nicholson
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
- University of Texas, Arlington, TX 76019, USA
| | - Marta Vargas
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Christian L Cox
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL 33199, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Michael L Logan
- Department of Biology, University of Nevada Reno, Reno, NV 89557, USA
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
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De León LF, Arias CF, Sharpe DMT, Bravo V, González R, Krahe R, Aguilar C. Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis. Mol Phylogenet Evol 2023; 189:107941. [PMID: 37804958 DOI: 10.1016/j.ympev.2023.107941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.
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Affiliation(s)
- Luis F De León
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA; Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama.
| | - Carlos F Arias
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington DC, USA
| | - Diana M T Sharpe
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Víctor Bravo
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
| | - Rigoberto González
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
| | - Rüdiger Krahe
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Celestino Aguilar
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), P. O. Box 0843-01103, Panamá, Panama; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa Ancón, Panamá, Panama
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Taboada BI, Zárate S, García-López R, Muñoz-Medina JE, Gómez-Gil B, Herrera-Estrella A, Sanchez-Flores A, Salas-Lais AG, Roche B, Martínez-Morales G, Domínguez Zárate H, Duque Molina C, Avilés Hernández R, López S, Arias CF. SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico. Microb Genom 2023; 9:001120. [PMID: 38112714 PMCID: PMC10763511 DOI: 10.1099/mgen.0.001120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/09/2023] [Indexed: 12/21/2023] Open
Abstract
In Mexico, the BA.4 and BA.5 Omicron variants dominated the fifth epidemic wave (summer 2022), superseding BA.2, which had circulated during the inter-wave period. The present study uses genome sequencing and statistical and phylogenetic analyses to examine these variants' abundance, distribution, and genetic diversity in Mexico from April to August 2022. Over 35 % of the sequenced genomes in this period corresponded to the BA.2 variant, 8 % to the BA.4 and 56 % to the BA.5 variant. Multiple subvariants were identified, but the most abundant, BA.2.9, BA.2.12.1, BA.5.1, BA.5.2, BA.5.2.1 and BA.4.1, circulated across the entire country, not forming geographical clusters. Contrastingly, other subvariants exhibited a geographically restricted distribution, most notably in the Southeast region, which showed a distinct subvariant dynamic. This study supports previous results showing that this region may be a significant entry point and contributed to introducing and evolving novel variants in Mexico. Furthermore, a differential distribution was observed for certain subvariants among specific States through time, which may have contributed to the overall increased diversity observed during this wave compared to the previous ones. This study highlights the importance of sustaining genomic surveillance to identify novel variants that may impact public health.
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Affiliation(s)
- Blanca Itzelt Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlan 82100, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36824, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Benjamin Roche
- Infectious Diseases: Vector, Control, Genetic, Ecology and Evolution (MIVEGEC) Université de Montpellier, IRD, CNRS, 34090 Montpellier, France
| | - Gabriela Martínez-Morales
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Hermilo Domínguez Zárate
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Célida Duque Molina
- Dirección de Prestaciones Médicas, Instituto Mexicano del Seguro Social, Ciudad de México 06700, Mexico
| | - Ricardo Avilés Hernández
- Unidad de Planeación e Innovación en Salud, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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Moreno-Contreras J, Espinoza MA, Cantú-Cuevas MA, Madrid-González DA, Barón-Olivares H, Ortiz-Orozco OD, Guzmán-Rodríguez C, Arias CF, Lopez S. Saliva sampling and its direct lysis is an excellent option for SARS-CoV-2 diagnosis in paediatric patients: comparison with the PanBio COVID-19 antigen rapid test in symptomatic and asymptomatic children. J Med Microbiol 2023; 72. [PMID: 38014762 DOI: 10.1099/jmm.0.001779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Introduction. Lateral flow test (LFTs) have been used as an alternative to reverse transcription quantitative PCR (RT-qPCR) in point-of-care testing. Despite their benefits, the sensitivity of LFTs may be low and is affected by several factors. We have previously reported the feasibility of using direct lysis of individual or pools of saliva samples from symptomatic and asymptomatic patients as a source of viral genomes for detection by RT-qPCR.Hypothesis. Direct lysed saliva is more sensitive than antigen tests to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in samples from children.Aim. Our goals here were to valuate the specificity and sensitivity of the PanBio COVID-19 antigen rapid test device (Ag-RTD) compared with RT-qPCR of direct lysed saliva.Methodology. We evaluated the performance of the PanBio COVID-19 Ag-RTD in comparison to RT-qPCR direct lysed saliva from paired samples of 256 symptomatic and 242 asymptomatic paediatric patients.Results. Overall, although there were no differences in the specificity (96.6%), we found a lower sensitivity (64.3%) of the PanBio Ag-test RTD compared to saliva in both symptomatic and asymptomatic patients. In addition, the sensitivity of PanBio was not correlated with the viral load present in the samples.Conclusion. Our data highlight the benefits of using RT-qPCR and saliva samples for SARS-CoV-2 detection, particularly in paediatric patients.
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Affiliation(s)
- Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Marco A Espinoza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Marco A Cantú-Cuevas
- Secretaría de Salud del Edo. de Morelos, Ajusco #2 Col. Buena Vista, Cuernavaca, Morelos, Mexico
| | - Daniel A Madrid-González
- Secretaría de Salud del Edo. de Morelos, Ajusco #2 Col. Buena Vista, Cuernavaca, Morelos, Mexico
| | - Héctor Barón-Olivares
- Servicios de Salud del Edo. de Morelos, Callejón Borda 3 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Oscar D Ortiz-Orozco
- Servicios de Salud del Edo. de Morelos, Callejón Borda 3 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Cecilia Guzmán-Rodríguez
- Servicios de Salud del Edo. de Morelos, Callejón Borda 3 Col. Centro, Cuernavaca, Morelos, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Susana Lopez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
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García-López R, Rivera-Gutiérrez X, Rosales-Rivera M, Zárate S, Muñoz-Medina JE, Roche B, Herrera-Estrella A, Gómez-Gil B, Sanchez-Flores A, Taboada B, Arias CF. SARS-CoV-2 BW lineage, a fast-growing Omicron variant from southeast Mexico bearing relevant escape mutations. Infection 2023; 51:1549-1555. [PMID: 37058241 PMCID: PMC10103656 DOI: 10.1007/s15010-023-02034-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 04/15/2023]
Abstract
PURPOSE The swift expansion of the BW.1 SARS-CoV-2 variant coincided with a rapid increase of COVID-19 cases occurring in Southeast Mexico in October, 2022, which marked the start of Mexico's sixth epidemiological wave. In Yucatan, up to 92% (58 of 73) of weekly sequenced genomes between epidemiological week 42 and 47 were identified as either BW.1 or its descendant, BW.1.1 in the region, during the last trimester of 2022. In the current study, a comprehensive genomic comparison was carried out to characterize the evolutionary history of the BW lineage, identifying its origins and its most important mutations. METHODS An alignment of all the genomes of the BW lineage and its parental BA.5.6.2 variant was carried out to identify their mutations. A phylogenetic and ancestral sequence reconstruction analysis with geographical inference, as well as a longitudinal analysis of point mutations, were performed to trace back their origin and contrast them with key RBD mutations in variant BQ.1, one of the fastest-growing lineages to date. RESULTS Our ancestral reconstruction analysis portrayed Mexico as the most probable origin of the BW.1 and BW.1.1 variants. Two synonymous substitutions, T7666C and C14599T, support their Mexican origin, whereas other two mutations are specific to BW.1: S:N460K and ORF1a:V627I. Two additional substitutions and a deletion are found in its descending subvariant, BW.1.1. Mutations found in the receptor binding domain, S:K444T, S:L452R, S:N460K, and S:F486V in BW.1 have been reported to be relevant for immune escape and are also key mutations in the BQ.1 lineage. CONCLUSIONS BW.1 appears to have arisen in the Yucatan Peninsula in Southeast Mexico sometime around July 2022 during the fifth COVID-19 wave. Its rapid growth may be in part explained by the relevant escape mutations also found in BQ.1.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Xaira Rivera-Gutiérrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Mauricio Rosales-Rivera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Benjamin Roche
- MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para La Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
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11
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Pérez-Juárez H, Serrano-Vázquez A, Godínez-Alvarez H, González E, Rojas-Velázquez L, Moran P, Portillo-Bobadilla T, Ramiro M, Hernández E, Lau C, Martínez M, Padilla MDLÁ, Zaragoza ME, Taboada B, Palomares LA, López S, Alagón A, Arias CF, Ximénez C. Longitudinal anti-SARS-CoV-2 antibody immune response in acute and convalescent patients. Front Cell Infect Microbiol 2023; 13:1239700. [PMID: 37743860 PMCID: PMC10515199 DOI: 10.3389/fcimb.2023.1239700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023] Open
Abstract
Despite global efforts to assess the early response and persistence of SARS-CoV-2 antibodies in patients infected with or recovered from COVID-19, our understanding of the factors affecting its dynamics remains limited. This work aimed to evaluate the early and convalescent immunity of outpatients infected with SARS-CoV-2 and to determine the factors that affect the dynamics and persistence of the IgM and IgG antibody response. Seropositivity of volunteers from Mexico City and the State of Mexico, Mexico, was evaluated by ELISA using the recombinant receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein for 90 days, at different time points (1, 15, 45, 60, and 90 days) after molecular diagnosis (RT-qPCR). Gender, age range, body mass index (BMI), comorbidities, and clinical spectrum of disease were analyzed to determine associations with the dynamics of anti-SARS-CoV-2 antibodies. On 90 days post-infection, individuals with moderate and asymptomatic disease presented the lowest levels of IgM, while for IgG, at the same time, the highest levels occurred with mild and moderate disease. The IgM and IgG levels were related to the clinical spectrum of disease, BMI, and the presence/absence of comorbidities through regression trees. The results suggest that the dynamics of anti-SARS-CoV-2 IgM and IgG antibodies in outpatients could be influenced by the clinical spectrum of the disease. In addition, the persistence of antibodies against SARS-CoV-2 could be related to the clinical spectrum of the disease, BMI, and the presence/absence of comorbidities.
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Affiliation(s)
- Horacio Pérez-Juárez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Estancias Posdoctorales por México-Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT), Mexico City, Mexico
| | - Angélica Serrano-Vázquez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Héctor Godínez-Alvarez
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico State, Mexico
| | - Enrique González
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Liliana Rojas-Velázquez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Patricia Moran
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Manuel Ramiro
- División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Eric Hernández
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Clara Lau
- Laboratorios de Análisis Clínicos e Imagenología, Biomédica de Referencia, S.A.P.I. DE C.V., Mexico City, Mexico
| | - Marcela Martínez
- Laboratorios de Análisis Clínicos e Imagenología, Biomédica de Referencia, S.A.P.I. DE C.V., Mexico City, Mexico
| | - Ma. de los Ángeles Padilla
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Martha E. Zaragoza
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, Mexico
| | - Laura A. Palomares
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, Mexico
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, Mexico
| | - Alejandro Alagón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, Mexico
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos, Mexico
| | - Cecilia Ximénez
- Laboratorio de Inmunología, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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12
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Ykema M, Ye K, Xun M, Harper J, Betancourt-Solis MA, Arias CF, McNew JA, Tao YJ. Human astrovirus capsid protein releases a membrane lytic peptide upon trypsin maturation. J Virol 2023; 97:e0080223. [PMID: 37504573 PMCID: PMC10506485 DOI: 10.1128/jvi.00802-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/13/2023] [Indexed: 07/29/2023] Open
Abstract
The human astrovirus (HAstV) is a non-enveloped, single-stranded RNA virus that is a common cause of gastroenteritis. Most non-enveloped viruses use membrane disruption to deliver the viral genome into a host cell after virus uptake. The virus-host factors that allow for HAstV cell entry are currently unknown but thought to be associated with the host-protease-mediated viral maturation. Using in vitro liposome disruption analysis, we identified a trypsin-dependent lipid disruption activity in the capsid protein of HAstV serotype 8. This function was further localized to the P1 domain of the viral capsid core, which was both necessary and sufficient for membrane disruption. Site-directed mutagenesis identified a cluster of four trypsin cleavage sites necessary to retain the lipid disruption activity, which is likely attributed to a short stretch of sequence ending at arginine 313 based on mass spectrometry of liposome-associated peptides. The membrane disruption activity was conserved across several other HAstVs, including the emerging VA2 strain, and effective against a wide range of lipid identities. This work provides key functional insight into the protease maturation process essential to HAstV infectivity and presents a method to investigate membrane penetration by non-enveloped viruses in vitro. IMPORTANCE Human astroviruses (HAstVs) are an understudied family of viruses that cause mild gastroenteritis but have recent cases associated with a more severe neural pathogenesis. Many important elements of the HAstV life cycle are not well understood, and further elucidating them can help understand the various forms of HAstV pathogenesis. In this study, we utilized an in vitro liposome-based assay to describe and characterize a previously unreported lipid disruption activity. This activity is dependent on the protease cleavage of key sites in HAstV capsid core and can be controlled by site-directed mutagenesis. Our group observed this activity in multiple strains of HAstV and in multiple lipid conditions, indicating this may be a conserved activity across the AstV family. The discovery of this function provides insight into HAstV cellular entry, pathogenesis, and a possible target for future therapeutics.
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Affiliation(s)
- Matthew Ykema
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Kai Ye
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Meng Xun
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Justin Harper
- Department of BioSciences, Rice University, Houston, Texas, USA
| | | | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - James A. McNew
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, Texas, USA
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13
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Castelán-Sánchez HG, Delaye L, Inward RPD, Dellicour S, Gutierrez B, Martinez de la Vina N, Boukadida C, Pybus OG, de Anda Jáuregui G, Guzmán P, Flores-Garrido M, Fontanelli Ó, Hernández Rosales M, Meneses A, Olmedo-Alvarez G, Herrera-Estrella AH, Sánchez-Flores A, Muñoz-Medina JE, Comas-García A, Gómez-Gil B, Zárate S, Taboada B, López S, Arias CF, Kraemer MUG, Lazcano A, Escalera Zamudio M. Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico. eLife 2023; 12:e82069. [PMID: 37498057 PMCID: PMC10431917 DOI: 10.7554/elife.82069] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/23/2023] [Indexed: 07/28/2023] Open
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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Affiliation(s)
- Hugo G Castelán-Sánchez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Programa de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y TecnologíaMexico CityMexico
| | - Luis Delaye
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Rhys PD Inward
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de BruxellesBruxellesBelgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU LeuvenLeuvenBelgium
| | - Bernardo Gutierrez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | | | - Celia Boukadida
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades RespiratoriasMexico CityMexico
| | - Oliver G Pybus
- Department of Biology, University of OxfordOxfordUnited Kingdom
- Department of Pathobiology, Royal Veterinary CollegeLondonUnited Kingdom
| | - Guillermo de Anda Jáuregui
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Programa de Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y TecnologíaMexico CityMexico
- Instituto Nacional de Medicina GenómicaMexico CityMexico
| | | | - Marisol Flores-Garrido
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Ciencias de la Computación, CINVESTAV-IPNMexico CityMexico
| | - Óscar Fontanelli
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Maribel Hernández Rosales
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Amilcar Meneses
- Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Ciencias de la Computación, CINVESTAV-IPNMexico CityMexico
| | - Gabriela Olmedo-Alvarez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Ingeniería Genética, CINVESTAV-Unidad IrapuatoGuanajuatoMexico
| | - Alfredo Heriberto Herrera-Estrella
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Laboratorio de expresión génica y desarrollo en hongos, CINVESTAV-Unidad IrapuatoIrapuatoMexico
| | - Alejandro Sánchez-Flores
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de MéxicoChamilpaMexico
| | - José Esteban Muñoz-Medina
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro SocialMexico CityMexico
| | - Andreu Comas-García
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Facultad de Medicina y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis PotosíSan Luis PotosíMexico
| | - Bruno Gómez-Gil
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Centro de Investigación en Alimentación y Desarrollo-CIAD, Unidad Regional Mazatlán en Acuicultura y Manejo AmbientalSinaloaMexico
| | - Selene Zárate
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de MéxicoMexico CityMexico
| | - Blanca Taboada
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Susana López
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Carlos F Arias
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Departamento de Genética del Desarrollo y Fisiología Molecular, Universidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Moritz UG Kraemer
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
| | - Antonio Lazcano
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Facultad de Ciencias, Universidad Nacional Autónoma de MéxicMexico CityMexico
| | - Marina Escalera Zamudio
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex)Mexico CityMexico
- Department of Biology, University of OxfordOxfordUnited Kingdom
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14
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Gómez-Romero N, Arias CF, Verdugo-Rodríguez A, López S, Valenzuela-Moreno LF, Cedillo-Peláez C, Basurto-Alcántara FJ. Immune protection induced by E2 recombinant glycoprotein of bovine viral diarrhea virus in a murine model. Front Vet Sci 2023; 10:1168846. [PMID: 37426077 PMCID: PMC10324609 DOI: 10.3389/fvets.2023.1168846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/30/2023] [Indexed: 07/11/2023] Open
Abstract
Bovine viral diarrhea virus (BVDV) is considered the most important viral pathogen in ruminants worldwide due to the broad range of clinical manifestations displayed by infected animals. Therefore, infection with BVDV leads to severe economic losses in several countries' beef and dairy industries. Vaccination prevents reproductive failure and gastrointestinal and respiratory disorders caused by BVDV infection. However, considering their limitations, conventional vaccines such as live, attenuated, and killed viruses have been applied. Hence, different studies have described subunit vaccines as an effective and safe alternative for BVDV protection. Therefore, in this study, the ectodomain of E2 (E2e) glycoprotein from NADL BVDV strain was expressed in mammalian cells and used in two vaccine formulations to evaluate immunogenicity and protection against BVDV conferred in a murine model. Formulations consisted of solo E2e glycoprotein and E2e glycoprotein emulsified in adjuvant ISA 61 VG. Five groups of 6 mice of 6-to-8-week-old were immunized thrice on days 1, 15, and 30 by intraperitoneal injection with the mentioned formulations and controls. To evaluate the conferred protection against BVDV, mice were challenged six weeks after the third immunization. In addition, the humoral immune response was evaluated after vaccination and challenge. Mice groups inoculated with solo E2e and the E2e + ISA 61 VG displayed neutralizing titers; however, the E2 antibody titers in the E2e + ISA 61 VG group were significantly higher than the mice group immunized with the solo E2e glycoprotein. In addition, immunization using E2e + ISA 61 VG prevents animals from developing severe lesions in surveyed tissues. Moreover, this group acquired protection against the BVDV challenge, evidenced by a significant reduction of positive staining for BVDV antigen in the lungs, liver, and brain between the experimental groups. Our findings demonstrated that using E2e + ISA 61 VG induces greater BVDV protection by an early humoral response and reduced histopathological lesions and BVDV antigen detection in affected organs, indicating that E2e + ISA 61 VG subunit formulation can be considered as a putative vaccine candidate against BVDV. The efficacy and safety of this vaccine candidate in cattle requires further investigation.
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Affiliation(s)
- Ninnet Gómez-Romero
- Vaccinology Laboratory, Department of Microbiology and Immunology, Facultad de Medicina Veterinaria y Zootecnia-Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Antonio Verdugo-Rodríguez
- Molecular Microbiology Laboratory, Department of Microbiology and Immunology, Facultad de Medicina Veterinaria y Zootecnia-Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Carlos Cedillo-Peláez
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Francisco Javier Basurto-Alcántara
- Vaccinology Laboratory, Department of Microbiology and Immunology, Facultad de Medicina Veterinaria y Zootecnia-Universidad Nacional Autónoma de México, Mexico City, Mexico
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15
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Zárate S, Taboada B, Rosales-Rivera M, García-López R, Muñoz-Medina JE, Sanchez-Flores A, Herrera-Estrella A, Gómez-Gil B, Selem Mojica N, Salas-Lais AG, Vazquez-Perez JA, Cabrera-Gaytán DA, Fernandes-Matano L, Uribe-Noguez LA, Chale-Dzul JB, Maldonado Meza BI, Mejía-Nepomuceno F, Pérez-Padilla R, Gutiérrez-Ríos RM, Loza A, Roche B, López S, Arias CF. Omicron-BA.1 Dispersion Rates in Mexico Varied According to the Regional Epidemic Patterns and the Diversity of Local Delta Subvariants. Viruses 2023; 15:243. [PMID: 36680283 PMCID: PMC9863047 DOI: 10.3390/v15010243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
PURPOSE The Omicron subvariant BA.1 of SARS-CoV-2 was first detected in November 2021 and quickly spread worldwide, displacing the Delta variant. In this work, a characterization of the spread of this variant in Mexico is presented. METHODS The time to fixation of BA.1, the diversity of Delta sublineages, the population density, and the level of virus circulation during the inter-wave interval were determined to analyze differences in BA.1 spread. RESULTS BA.1 began spreading during the first week of December 2021 and became dominant in the next three weeks, causing the fourth COVID-19 epidemiological surge in Mexico. Unlike previous variants, BA.1 did not exhibit a geographically distinct circulation pattern. However, a regional difference in the speed of the replacement of the Delta variant was observed. CONCLUSIONS Viral diversity and the relative abundance of the virus in a particular area around the time of the introduction of a new lineage seem to have influenced the spread dynamics, in addition to population density. Nonetheless, if there is a significant difference in the fitness of the variants, or if the time allowed for the competition is sufficiently long, it seems the fitter virus will eventually become dominant, as observed in the eventual dominance of the BA.1.x variant in Mexico.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Mauricio Rosales-Rivera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica Para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato 36821, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlan 82100, Mexico
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia 58089, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Joel Armando Vazquez-Perez
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - David Alejandro Cabrera-Gaytán
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Larissa Fernandes-Matano
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico
| | - Luis Antonio Uribe-Noguez
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Mexico City, 02990, Mexico
| | - Juan Bautista Chale-Dzul
- Unidad de Investigación Médica Yucatán, Instituto Mexicano del Seguro Social, Merida 97150, Mexico
| | | | - Fidencio Mejía-Nepomuceno
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - Rogelio Pérez-Padilla
- Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, México City 14080, Mexico
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Benjamin Roche
- Infectious Diseases: Vector, Control, Genetic, Ecology and Evolution (MIVEGEC) Université de Montpellier, IRD, CNRS, 34090 Montpellier, France
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
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16
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Loza A, Wong-Chew RM, Jiménez-Corona ME, Zárate S, López S, Ciria R, Palomares D, García-López R, Iša P, Taboada B, Rosales M, Boukadida C, Herrera-Estrella A, Mojica NS, Rivera-Gutierrez X, Muñoz-Medina JE, Salas-Lais AG, Sanchez-Flores A, Vazquez-Perez JA, Arias CF, Gutiérrez-Ríos RM. Two-year follow-up of the COVID-19 pandemic in Mexico. Front Public Health 2023; 10:1050673. [PMID: 36711379 PMCID: PMC9880891 DOI: 10.3389/fpubh.2022.1050673] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Background After the initial outbreak in China (December 2019), the World Health Organization declared COVID-19 a pandemic on March 11th, 2020. This paper aims to describe the first 2 years of the pandemic in Mexico. Design and methods This is a population-based longitudinal study. We analyzed data from the national COVID-19 registry to describe the evolution of the pandemic in terms of the number of confirmed cases, hospitalizations, deaths and reported symptoms in relation to health policies and circulating variants. We also carried out logistic regression to investigate the major risk factors for disease severity. Results From March 2020 to March 2022, the coronavirus disease 2019 (COVID-19) pandemic in Mexico underwent four epidemic waves. Out of 5,702,143 confirmed cases, 680,063 were hospitalized (11.9%), and 324,436 (5.7%) died. Even if there was no difference in susceptibility by gender, males had a higher risk of death (CFP: 7.3 vs. 4.2%) and hospital admission risk (HP: 14.4 vs. 9.5%). Severity increased with age. With respect to younger ages (0-17 years), the 60+ years or older group reached adjusted odds ratios of 9.63 in the case of admission and 53.05 (95% CI: 27.94-118.62) in the case of death. The presence of any comorbidity more than doubled the odds ratio, with hypertension-diabetes as the riskiest combination. While the wave peaks increased over time, the odds ratios for developing severe disease (waves 2, 3, and 4 to wave 1) decreased to 0.15 (95% CI: 0.12-0.18) in the fourth wave. Conclusion The health policy promoted by the Mexican government decreased hospitalizations and deaths, particularly among older adults with the highest risk of admission and death. Comorbidities augment the risk of developing severe illness, which is shown to rise by double in the Mexican population, particularly for those reported with hypertension-diabetes. Factors such as the decrease in the severity of the SARS-CoV2 variants, changes in symptomatology, and advances in the management of patients, vaccination, and treatments influenced the decrease in mortality and hospitalizations.
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Affiliation(s)
- Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rosa María Wong-Chew
- Facultad de Medicina, Laboratorio de Investigación en Enfermedades Infecciosas, División de Investigación, Universidad Nacional Autónoma de Mexico, Ciudad de México, Mexico
| | | | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Ricardo Ciria
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Diego Palomares
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Mauricio Rosales
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Alfredo Herrera-Estrella
- Centro de Investigación y de Estudios Avanzados del IPN, Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Irapuato, Guanajuato, Mexico
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Michoacan, Mexico
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - José Esteba Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico,*Correspondence: Rosa María Gutiérrez-Ríos ✉
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17
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Delgado-Cunningham K, López T, Khatib F, Arias CF, DuBois RM. Structure of the divergent human astrovirus MLB capsid spike. Structure 2022; 30:1573-1581.e3. [PMID: 36417907 PMCID: PMC9722636 DOI: 10.1016/j.str.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/30/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Despite their worldwide prevalence and association with human disease, the molecular bases of human astrovirus (HAstV) infection and evolution remain poorly characterized. Here, we report the structure of the capsid protein spike of the divergent HAstV MLB clade (HAstV MLB). While the structure shares a similar folding topology with that of classical-clade HAstV spikes, it is otherwise strikingly different. We find no evidence of a conserved receptor-binding site between the MLB and classical HAstV spikes, suggesting that MLB and classical HAstVs utilize different receptors for host-cell attachment. We provide evidence for this hypothesis using a novel HAstV infection competition assay. Comparisons of the HAstV MLB spike structure with structures predicted from its sequence reveal poor matches, but template-based predictions were surprisingly accurate relative to machine-learning-based predictions. Our data provide a foundation for understanding the mechanisms of infection by diverse HAstVs and can support structure determination in similarly unstudied systems.
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Affiliation(s)
- Kevin Delgado-Cunningham
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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18
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Iša P, Taboada B, García-López R, Boukadida C, Ramírez-González JE, Vázquez-Pérez JA, Hernández-Terán A, Romero-Espinoza JÁ, Muñoz-Medina JE, Grajales-Muñiz C, Rincón-Rubio A, Matías-Florentino M, Sanchez-Flores A, Mendieta-Condado E, Barrera-Badillo G, López S, Hernández-Rivas L, López-Martínez I, Ávila-Ríos S, Arias CF. Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease. BMC Infect Dis 2022; 22:792. [PMID: 36261802 PMCID: PMC9580447 DOI: 10.1186/s12879-022-07783-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/06/2022] [Indexed: 11/22/2022] Open
Abstract
Background SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized.
Methods In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. Results Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. Conclusions Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07783-8.
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Affiliation(s)
- Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | | | | | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Concepción Grajales-Muñiz
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alma Rincón-Rubio
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Ciudad de Mexico, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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19
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Sanluis-Verdes A, Colomer-Vidal P, Rodriguez-Ventura F, Bello-Villarino M, Spinola-Amilibia M, Ruiz-Lopez E, Illanes-Vicioso R, Castroviejo P, Aiese Cigliano R, Montoya M, Falabella P, Pesquera C, Gonzalez-Legarreta L, Arias-Palomo E, Solà M, Torroba T, Arias CF, Bertocchini F. Wax worm saliva and the enzymes therein are the key to polyethylene degradation by Galleria mellonella. Nat Commun 2022; 13:5568. [PMID: 36195604 PMCID: PMC9532405 DOI: 10.1038/s41467-022-33127-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/02/2022] [Indexed: 11/20/2022] Open
Abstract
Plastic degradation by biological systems with re-utilization of the by-products could be a future solution to the global threat of plastic waste accumulation. Here, we report that the saliva of Galleria mellonella larvae (wax worms) is capable of oxidizing and depolymerizing polyethylene (PE), one of the most produced and sturdy polyolefin-derived plastics. This effect is achieved after a few hours’ exposure at room temperature under physiological conditions (neutral pH). The wax worm saliva can overcome the bottleneck step in PE biodegradation, namely the initial oxidation step. Within the saliva, we identify two enzymes, belonging to the phenol oxidase family, that can reproduce the same effect. To the best of our knowledge, these enzymes are the first animal enzymes with this capability, opening the way to potential solutions for plastic waste management through bio-recycling/up-cycling. The crucial first step in the biodegradation of polyethylene plastic is oxidation of the polymer. This has traditionally required abiotic pre-treatment, but now Bertocchini and colleagues report two wax worm enzymes capable of catalyzing this oxidation and subsequent degradation at room temperature.
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Affiliation(s)
- A Sanluis-Verdes
- Centro de Investigaciones Biologicas-Margarita Salas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Department of Plant and Microbial Biology, Madrid, Spain
| | - P Colomer-Vidal
- Centro de Investigaciones Biologicas-Margarita Salas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Department of Plant and Microbial Biology, Madrid, Spain
| | - F Rodriguez-Ventura
- Centro de Investigaciones Biologicas-Margarita Salas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Department of Plant and Microbial Biology, Madrid, Spain
| | - M Bello-Villarino
- Centro de Investigaciones Biologicas-Margarita Salas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Department of Plant and Microbial Biology, Madrid, Spain
| | | | - E Ruiz-Lopez
- Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB)-CSIC, Barcelona, Spain
| | - R Illanes-Vicioso
- Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB)-CSIC, Barcelona, Spain
| | - P Castroviejo
- Department of Chemistry, Faculty of Science and PCT, University of Burgos, Burgos, Spain
| | | | - M Montoya
- CIB-CSIC, Department of Molecular Biomedicine, Madrid, Spain
| | - P Falabella
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - C Pesquera
- Department of Chemistry and Process & Resource Engineering, Inorganic Chemistry Group-University of Cantabria, Nanomedicine-IDIVAL, Santander, Spain
| | - L Gonzalez-Legarreta
- Department of Chemistry and Process & Resource Engineering, Inorganic Chemistry Group-University of Cantabria, Nanomedicine-IDIVAL, Santander, Spain
| | - E Arias-Palomo
- CIB-CSIC, Department of Structural and Chemical Biology, Madrid, Spain
| | - M Solà
- Department of Structural Biology, Molecular Biology Institute of Barcelona (IBMB)-CSIC, Barcelona, Spain
| | - T Torroba
- Department of Chemistry, Faculty of Science and PCT, University of Burgos, Burgos, Spain
| | - C F Arias
- Centro de Investigaciones Biologicas-Margarita Salas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Department of Plant and Microbial Biology, Madrid, Spain.
| | - F Bertocchini
- Centro de Investigaciones Biologicas-Margarita Salas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Department of Plant and Microbial Biology, Madrid, Spain.
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20
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Zárate S, Taboada B, Muñoz-Medina JE, Iša P, Sanchez-Flores A, Boukadida C, Herrera-Estrella A, Selem Mojica N, Rosales-Rivera M, Gómez-Gil B, Salas-Lais AG, Santacruz-Tinoco CE, Montoya-Fuentes H, Alvarado-Yaah JE, Molina-Salinas GM, Espinoza-Ayala GE, Enciso-Moreno JA, Gutiérrez-Ríos RM, Loza A, Moreno-Contreras J, García-López R, Rivera-Gutierrez X, Comas-García A, Wong-Chew RM, Jiménez-Corona ME, del Angel RM, Vazquez-Perez JA, Matías-Florentino M, Pérez-García M, Ávila-Ríos S, Castelán-Sánchez HG, Delaye L, Martínez-Castilla LP, Escalera-Zamudio M, López S, Arias CF. The Alpha Variant (B.1.1.7) of SARS-CoV-2 Failed to Become Dominant in Mexico. Microbiol Spectr 2022; 10:e0224021. [PMID: 35389245 PMCID: PMC9045257 DOI: 10.1128/spectrum.02240-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/17/2022] [Indexed: 12/26/2022] Open
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, the emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first identified in the United Kingdom in September 2020, was well documented in different areas of the world and became a global public health concern because of its increased transmissibility. The B.1.1.7 lineage was first detected in Mexico during December 2020, showing a slow progressive increase in its circulation frequency, which reached its maximum in May 2021 but never became predominant. In this work, we analyzed the patterns of diversity and distribution of this lineage in Mexico using phylogenetic and haplotype network analyses. Despite the reported increase in transmissibility of the B.1.1.7 lineage, in most Mexican states, it did not displace cocirculating lineages, such as B.1.1.519, which dominated the country from February to May 2021. Our results show that the states with the highest prevalence of B.1.1.7 were those at the Mexico-U.S. border. An apparent pattern of dispersion of this lineage from the northern states of Mexico toward the center or the southeast was observed in the largest transmission chains, indicating possible independent introduction events from the United States. However, other entry points cannot be excluded, as shown by multiple introduction events. Local transmission led to a few successful haplotypes with a localized distribution and specific mutations indicating sustained community transmission. IMPORTANCE The emergence and rapid increase of the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the world were due to its increased transmissibility. However, it did not displace cocirculating lineages in most of Mexico, particularly B.1.1.519, which dominated the country from February to May 2021. In this work, we analyzed the distribution of B.1.1.7 in Mexico using phylogenetic and haplotype network analyses. Our results show that the states with the highest prevalence of B.1.1.7 (around 30%) were those at the Mexico-U.S. border, which also exhibited the highest lineage diversity, indicating possible introduction events from the United States. Also, several haplotypes were identified with a localized distribution and specific mutations, indicating that sustained community transmission occurred in the country.
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Affiliation(s)
- Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México, México
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, México
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, México
| | - Mauricio Rosales-Rivera
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlám, Mazatlán, México
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Héctor Montoya-Fuentes
- Centro de Investigación Biomedica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, México
| | - Julio Elias Alvarado-Yaah
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | | | - José Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano del Seguro Social, Zacatecas, Zacatecas, México
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Andreu Comas-García
- Facultad de Medicna y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Rosa María Wong-Chew
- Facultad de Medicina, Laboratorio de Investigación en Enfermedades Infecciosas, División de Investigación, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Rosa María del Angel
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav, Ciudad de México, México
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Marissa Pérez-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, México
| | - Hugo G. Castelán-Sánchez
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Luis Delaye
- Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, Guanajuato, México
| | - León P. Martínez-Castilla
- Programa de Investigadoras e investigadores por México Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | | | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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21
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Moreno-Contreras J, Espinoza MA, Sandoval-Jaime C, Cantú-Cuevas MA, Madrid-González DA, Barón-Olivares H, Ortiz-Orozco OD, Muñoz-Rangel AV, Guzmán-Rodríguez C, Hernández-de la Cruz M, Eroza-Osorio CM, Arias CF, López S. Pooling saliva samples as an excellent option to increase the surveillance for SARS-CoV-2 when re-opening community settings. PLoS One 2022; 17:e0263114. [PMID: 35077513 PMCID: PMC8789121 DOI: 10.1371/journal.pone.0263114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
In many countries a second wave of infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has occurred, triggering a shortage of reagents needed for diagnosis and compromising the capacity of laboratory testing. There is an urgent need to develop methods to accelerate the diagnostic procedures. Pooling samples represents a strategy to overcome the shortage of reagents, since several samples can be tested using one reaction, significantly increasing the number and speed with which tests can be carried out. We have reported the feasibility to use a direct lysis procedure of saliva as source for RNA to SARS-CoV-2 genome detection by reverse transcription quantitative-PCR (RT-qPCR). Here, we show that the direct lysis of saliva pools, of either five or ten samples, does not compromise the detection of viral RNA. In addition, it is a sensitive, fast, and inexpensive method that can be used for massive screening, especially considering the proximity of the reincorporation of activities in universities, offices, and schools.
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Affiliation(s)
- Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | - Marco A. Espinoza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | - Carlos Sandoval-Jaime
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | | | | | | | | | | | | | | | | | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología UNAM, Cuernavaca, Morelos, México
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22
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Taboada B, Zárate S, Iša P, Boukadida C, Vazquez-Perez JA, Muñoz-Medina JE, Ramírez-González JE, Comas-García A, Grajales-Muñiz C, Rincón-Rubio A, Matías-Florentino M, Sanchez-Flores A, Mendieta-Condado E, Verleyen J, Barrera-Badillo G, Hernández-Rivas L, Mejía-Nepomuceno F, Martínez-Orozco JA, Becerril-Vargas E, López S, López-Martínez I, Ávila-Ríos S, Arias CF. Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic. Viruses 2021; 13:2161. [PMID: 34834967 PMCID: PMC8622467 DOI: 10.3390/v13112161] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/09/2021] [Accepted: 10/19/2021] [Indexed: 12/21/2022] Open
Abstract
During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.
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Affiliation(s)
- Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 03100, Mexico;
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Joel Armando Vazquez-Perez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - José Esteban Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico;
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Andreu Comas-García
- Facultad de Medicina y Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78120, Mexico;
| | - Concepción Grajales-Muñiz
- Coordinación de Control Técnico de Insumos, Instituto Mexicano del Seguro Social, Mexico City 07760, Mexico;
| | - Alma Rincón-Rubio
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (A.S.-F.); (J.V.)
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Jerome Verleyen
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (A.S.-F.); (J.V.)
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Fidencio Mejía-Nepomuceno
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - José Arturo Martínez-Orozco
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - Eduardo Becerril-Vargas
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.A.V.-P.); (F.M.-N.); (J.A.M.-O.); (E.B.-V.)
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City 01480, Mexico; (J.E.R.-G.); (E.M.-C.); (G.B.-B.); (L.H.-R.); (I.L.-M.)
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (C.B.); (A.R.-R.); (M.M.-F.); (S.Á.-R.)
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (B.T.); (P.I.); (S.L.)
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23
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Arias CF, Dikow RB, McMillan WO, De León LF. De Novo Genome Assembly of the Electric Fish Brachyhypopomus occidentalis (Hypopomidae, Gymnotiformes). Genome Biol Evol 2021; 13:6377337. [PMID: 34581791 PMCID: PMC8536545 DOI: 10.1093/gbe/evab223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
The bluntnose knifefish Brachyhypopomus occidentalis is a primary freshwater fish from north-western South America and Lower Central America. Like other Gymnotiformes, it has an electric organ that generates electric discharges used for both communication and electrolocation. We assembled a high-quality reference genome sequence of B. occidentalis by combining Oxford Nanopore and 10X Genomics linked-reads technologies. We also describe its demographic history in the context of the rise of the Isthmus of Panama. The size of the assembled genome is 540.3 Mb with an N50 scaffold length of 5.4 Mb, which includes 93.8% complete, 0.7% fragmented, and 5.5% of missing vertebrate/Actinoterigie Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 11.04% of the genome, and 34,347 protein-coding genes were predicted, of which 23,935 have been functionally annotated. Demographic analysis suggests a rapid effective population expansion between 3 and 5 Myr, corresponding to the final closure of the Isthmus of Panama (2.8–3.5 Myr). This event was followed by a sudden and constant population decline during the last 1 Myr, likely associated with strong shifts in both precipitation and sea level during the Pleistocene glacial-interglacial cycles. The de novo genome assembly of B. occidentalis will provide novel insights into the molecular basis of both electric signal productions and detection and will be fundamental for understanding the processes that have shaped the diversity of Neotropical freshwater environments.
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Affiliation(s)
- Carlos F Arias
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA.,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA.,Smithsonian Tropical Research Institute, Panamá, Panamá
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia, USA
| | | | - Luis F De León
- Department of Biology, University of Massachusetts, Boston, Massachusetts, USA.,Smithsonian Tropical Research Institute, Panamá, Panamá.,Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Panamá, Panamá
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24
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Rodríguez-Maldonado AP, Vázquez-Pérez JA, Cedro-Tanda A, Taboada B, Boukadida C, Wong-Arámbula C, Nuñez-García TE, Cruz-Ortiz N, Barrera-Badillo G, Hernández-Rivas L, López-Martínez I, Mendoza-Vargas A, Reyes-Grajeda JP, Alcaraz N, Peñaloza-Figueroa F, Gonzalez-Barrera D, Rangel-DeLeon D, Herrera-Montalvo LA, Mejía-Nepomuceno F, Hernández-Terán A, Mújica-Sánchez M, Becerril-Vargas E, Martínez-Orozco JA, Pérez-Padilla R, Salas-Hernández J, Sanchez-Flores A, Isa P, Matías-Florentino M, Ávila-Ríos S, Muñoz-Medina JE, Grajales-Muñiz C, Salas-Lais AG, Santos Coy-Arechavaleta A, Hidalgo-Miranda A, Arias CF, Ramírez-González JE. Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico. Arch Virol 2021; 166:3173-3177. [PMID: 34448936 PMCID: PMC8390838 DOI: 10.1007/s00705-021-05208-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.
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Affiliation(s)
- Abril Paulina Rodríguez-Maldonado
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Claudia Wong-Arámbula
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Tatiana Ernestina Nuñez-García
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Natividad Cruz-Ortiz
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Gisela Barrera-Badillo
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Lucía Hernández-Rivas
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | - Irma López-Martínez
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico
| | | | | | - Nicolas Alcaraz
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | | | | | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico
| | | | | | | | | | | | - Carlos F Arias
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Mexico City, Mexico.
| | - José Ernesto Ramírez-González
- Dirección General de Epidemiología, Instituto de Diagnóstico y Referencia Epidemiológicos "Dr. Manuel Martínez Báez, Mexico City, Mexico.
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25
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Abstract
Rotaviruses are important agents of severe gastroenteritis in young children, and show a very selective cell and tissue tropism, as well as significant age and host restriction. In the last few years, these properties have been associated with the initial interaction of the virus with histo-blood group antigens on the cell surface, although post-attachment interactions have also been found to define the susceptibility to infection of human enteroids. These initial interactions seem also to determine the virus entry pathway, as well as the induction of signaling cascades that influence the virus intracellular vesicular traffic and escape from endosomes. Here we review the current knowledge of the different stages of the virus entry journey.
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Affiliation(s)
- Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, Mexico.
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, Mexico
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Taboada B, Morán P, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximenez C, Arias CF. The gut virome of healthy children during the first year of life is diverse and dynamic. PLoS One 2021; 16:e0240958. [PMID: 33852569 PMCID: PMC8046192 DOI: 10.1371/journal.pone.0240958] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
In this work, we determined the diversity and dynamics of the gut virome of infants during the first year of life. Fecal samples were collected monthly, from birth to one year of age, from three healthy children living in a semi-rural village in Mexico. Most of the viral reads were classified into six families of bacteriophages including five dsDNA virus families of the order Caudovirales, with Siphoviridae and Podoviridae being the most abundant. Eukaryotic viruses were detected as early as two weeks after birth and remained present all along the first year of life. Thirty-four different eukaryotic virus families were found, where eight of these families accounted for 98% of all eukaryotic viral reads: Anelloviridae, Astroviridae, Caliciviridae, Genomoviridae, Parvoviridae, Picornaviridae, Reoviridae and the plant-infecting viruses of the Virgaviridae family. Some viruses in these families are known human pathogens, and it is surprising that they were found during the first year of life in infants without gastrointestinal symptoms. The eukaryotic virus species richness found in this work was higher than that observed in previous studies; on average between 7 and 24 virus species were identified per sample. The richness and abundance of the eukaryotic virome significantly increased during the second semester of life, probably because of an increased environmental exposure of infants with age. Our findings suggest an early and permanent contact of infants with a diverse array of bacteriophages and eukaryotic viruses, whose composition changes over time. The bacteriophages and eukaryotic viruses found in these children could represent a metastable virome, whose potential influence on the development of the infant's immune system or on the health of the infants later in life, remains to be investigated.
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Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Cecilia Ximenez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail: (CFA); (CX); (JT)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (CFA); (CX); (JT)
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Aguilar-Hernández N, Meyer L, López S, DuBois RM, Arias CF. Protein Disulfide Isomerase A4 Is Involved in Genome Uncoating during Human Astrovirus Cell Entry. Viruses 2020; 13:v13010053. [PMID: 33396308 PMCID: PMC7824429 DOI: 10.3390/v13010053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
Although human astroviruses (HAstVs) are important agents of gastroenteritis in young children, the studies aimed at characterizing their biology have been limited, in particular regarding their cell entry process. It has been shown that HAstV serotype 8 enters human cells by a classical clathrin-mediated endocytosis pathway; however, the cell receptor or other cell entry factors that may be relevant for an efficient viral infection are unknown. In this work we used a far-Western blotting approach to identify cellular proteins that interact with the recombinant capsid spike proteins of HAstV serotypes 1, 2, and 8, synthesized in Escherichia coli. We identified the 72 kDa protein disulfide isomerase A4 (PDIA4) as a binding partner for HAstV-1 and -8 spikes, but not for the HAstV-2 spike. In agreement with this observation, the PDI inhibitor 16F16 strongly blocked infection by HAstV serotypes 1 and 8, but not serotype 2. RNA interference of PDIA4 expression selectively blocked HAstV-8 infectivity. We also showed that the PDI activity does not affect virus binding or internalization but is required for uncoating of the viral genome.
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Affiliation(s)
- Nayeli Aguilar-Hernández
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (N.A.-H.); (S.L.)
| | - Lena Meyer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA; (L.M.); (R.M.D.)
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (N.A.-H.); (S.L.)
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA; (L.M.); (R.M.D.)
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (N.A.-H.); (S.L.)
- Correspondence:
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Moreno-Contreras J, Espinoza MA, Sandoval-Jaime C, Cantú-Cuevas MA, Barón-Olivares H, Ortiz-Orozco OD, Muñoz-Rangel AV, Hernández-de la Cruz M, Eroza-Osorio CM, Arias CF, López S. Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages. J Clin Microbiol 2020; 58:e01659-20. [PMID: 32703816 PMCID: PMC7512180 DOI: 10.1128/jcm.01659-20] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022] Open
Abstract
As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Detection of the viral genome through reverse transcription-quantitative PCR (RT-qPCR) is the gold standard for this virus; however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is less expensive and can be as efficient as the classical protocol, which involves column purification of the viral RNA. In addition, it bypasses the need for swab sampling, decreases the risk of the health care personnel involved in the testing process, and accelerates the diagnostic procedure.
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Affiliation(s)
- Joaquín Moreno-Contreras
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Marco A Espinoza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos Sandoval-Jaime
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | | | | | | | | | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Castillo AM, Saltonstall K, Arias CF, Chavarria KA, Ramírez-Camejo LA, Mejía LC, De León LF. The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification. Insects 2020; 11:insects11090578. [PMID: 32878094 PMCID: PMC7565411 DOI: 10.3390/insects11090578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023]
Abstract
Simple Summary Insects host a highly diverse bacterial community. Although we have a good understanding of the role that this microbiome plays in insects, the composition and diversity of microbiomes associated with Neotropical freshwater insects is virtually unknown. Here, we describe, for the first time, the microbiome associated with six species of Neotropical water striders in Panama. We also performed phylogenetic analyses to explore potential codiversification or coevolution between water strider species and their associated microbiome. We found a diverse microbiome associated with the six species of water striders, with the dominant bacterial taxa belonging to the phyla Proteobacteria and Tenericutes. Although some bacterial lineages were shared across species, some lineages were also uniquely associated with different water strider species. Our results suggest that both environmental variation and host phylogenetic identity are important drivers of the microbiome associated with water striders. Understanding the evolution of the host-microbiome interaction is crucial to our understanding of Neotropical freshwater ecosystems. Abstract Insects host a highly diverse microbiome, which plays a crucial role in insect life. However, the composition and diversity of microbiomes associated with Neotropical freshwater insects is virtually unknown. In addition, the extent to which diversification of this microbiome is associated with host phylogenetic divergence remains to be determined. Here, we present the first comprehensive analysis of bacterial communities associated with six closely related species of Neotropical water striders in Panama. We used comparative phylogenetic analyses to assess associations between dominant bacterial linages and phylogenetic divergence among species of water striders. We found a total of 806 16S rRNA amplicon sequence variants (ASVs), with dominant bacterial taxa belonging to the phyla Proteobacteria (76.87%) and Tenericutes (19.51%). Members of the α- (e.g., Wolbachia) and γ- (e.g., Acinetobacter, Serratia) Proteobacteria, and Mollicutes (e.g., Spiroplasma) were predominantly shared across species, suggesting the presence of a core microbiome in water striders. However, some bacterial lineages (e.g., Fructobacillus, Fluviicola and Chryseobacterium) were uniquely associated with different water strider species, likely representing a distinctive feature of each species’ microbiome. These findings indicate that both host identity and environmental context are important drivers of microbiome diversity in water striders. In addition, they suggest that diversification of the microbiome is associated with diversification in water striders. Although more research is needed to establish the evolutionary consequences of host-microbiome interaction in water striders, our findings support recent work highlighting the role of bacterial community host-microbiome codiversification.
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Affiliation(s)
- Anakena M. Castillo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103 Panamá 5, Panama; (A.M.C.); (L.A.R.-C.); (L.C.M.)
- Department of Biotechnology, Acharya Nagarjuna University, Guntur 522 510, Andhra Pradesh, India
| | - Kristin Saltonstall
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092 Amador, Naos, Panama; (K.S.); (C.F.A.); (K.A.C.)
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092 Amador, Naos, Panama; (K.S.); (C.F.A.); (K.A.C.)
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Karina A. Chavarria
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092 Amador, Naos, Panama; (K.S.); (C.F.A.); (K.A.C.)
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720, USA
| | - Luis A. Ramírez-Camejo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103 Panamá 5, Panama; (A.M.C.); (L.A.R.-C.); (L.C.M.)
- Coiba Scientific Station (COIBA-AIP), City of Knowledge, P.O. Box 0843-01853 Balboa, Panama
| | - Luis C. Mejía
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103 Panamá 5, Panama; (A.M.C.); (L.A.R.-C.); (L.C.M.)
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092 Amador, Naos, Panama; (K.S.); (C.F.A.); (K.A.C.)
| | - Luis F. De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103 Panamá 5, Panama; (A.M.C.); (L.A.R.-C.); (L.C.M.)
- Smithsonian Tropical Research Institute, P.O. Box 0843-03092 Amador, Naos, Panama; (K.S.); (C.F.A.); (K.A.C.)
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
- Coiba Scientific Station (COIBA-AIP), City of Knowledge, P.O. Box 0843-01853 Balboa, Panama
- Correspondence:
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30
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Taboada B, Vazquez-Perez JA, Muñoz-Medina JE, Ramos-Cervantes P, Escalera-Zamudio M, Boukadida C, Sanchez-Flores A, Isa P, Mendieta-Condado E, Martínez-Orozco JA, Becerril-Vargas E, Salas-Hernández J, Grande R, González-Torres C, Gaytán-Cervantes FJ, Vazquez G, Pulido F, Araiza-Rodríguez A, Garcés-Ayala F, González-Bonilla CR, Grajales-Muñiz C, Borja-Aburto VH, Barrera-Badillo G, López S, Hernández-Rivas L, Perez-Padilla R, López-Martínez I, Ávila-Ríos S, Ruiz-Palacios G, Ramírez-González JE, Arias CF. Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico. J Virol 2020; 94:e01056-20. [PMID: 32641486 PMCID: PMC7459550 DOI: 10.1128/jvi.01056-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/07/2020] [Indexed: 11/20/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts.IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.
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Affiliation(s)
- Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - José Esteban Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
| | - José A Martínez-Orozco
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | - Jorge Salas-Hernández
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Ricardo Grande
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carolina González-Torres
- División de Desarrollo de la Investigación, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Gloria Vazquez
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Francisco Pulido
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Adnan Araiza-Rodríguez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
| | - Fabiola Garcés-Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
| | | | - Concepción Grajales-Muñiz
- Coordinación de Control Técnico de Insumos, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Lucía Hernández-Rivas
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
| | - Rogelio Perez-Padilla
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Irma López-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | | | | | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Aguado-García Y, Taboada B, Morán P, Rivera-Gutiérrez X, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximénez C, Arias CF. Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life. Sci Rep 2020; 10:13595. [PMID: 32788688 PMCID: PMC7423923 DOI: 10.1038/s41598-020-70684-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
Plant viruses have been reported to be common in the gut of human adults, presumably as result of food ingestion. In this work, we report that plant viruses can also be found frequently in the gut and oropharynx of children during their first year of life, even when they are exclusively breast-fed. Fecal and oropharynx samples were collected monthly, from birth to 1 year of age, from three apparently healthy children in a semi-rural community and analyzed by next generation sequencing. In 100% of the fecal samples and 65% of the oropharynx samples at least one plant virus was identified. Tobamoviruses in the Virgaviridae family were by far the most frequently detected, with tropical soda apple mosaic virus, pepper mild mottle virus, and opuntia tobamovirus 2 being the most common species. Seventeen complete virus genomes could be assembled, and phylogenetic analyses showed a large diversity of virus strains circulating in the population. These results suggest that children are continuously exposed to an extensive and highly diverse collection of tobamoviruses. Whether the common presence of plant viruses at an early age influences the infant's immune system, either directly or through interaction with other members of the microbiota, remains to be investigated.
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Affiliation(s)
- Yarenci Aguado-García
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Patricia Morán
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Xaira Rivera-Gutiérrez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Angélica Serrano-Vázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Pavel Iša
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Rojas-Velázquez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Horacio Pérez-Juárez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06726, Cuauhtémoc, Ciudad de México, Mexico.
| | - Cecilia Ximénez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Dr. Balmis Num. 148 Doctores, 06726, Ciudad de México, Mexico.
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, 62210, Cuernavaca, Morelos, Mexico.
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32
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López S, Arias CF. [Rotavirus genomics. Public health impact]. Salud Publica Mex 2020; 62:36-41. [PMID: 31869559 DOI: 10.21149/9965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
With the introduction of rotavirus vaccines Rotarix (RV1) or RotaTeq (RV5) in the immunization programs of an increasing number of countries, there is concern that the immune selection pressure induced will cause an increase in the prevalence of virus genotypes not included in the vaccine formulation, or to the appearance of novel rotavirus strains that could evade the protective immune response. The natural fluctuation of rotaviruses makes it difficult to distinguish if the change in the circulating strains is due to the vaccine selective pressure or to the natural diversity fluctuation of viruses. If there has been a selective pressure, it has been low so far. However, it is important to keep an epidemiological surveillance and pay attention to the emergence of strains that are resistant to the vaccine, in particular in those countries where the viral diversity has been shown to be higher.
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Affiliation(s)
- Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, México
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, México
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Iša P, Pérez-Delgado A, Quevedo IR, López S, Arias CF. Rotaviruses Associate with Distinct Types of Extracellular Vesicles. Viruses 2020; 12:v12070763. [PMID: 32708544 PMCID: PMC7411906 DOI: 10.3390/v12070763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/29/2022] Open
Abstract
Rotaviruses are the leading cause of viral gastroenteritis among children under five years of age. Rotavirus cell entry has been extensively studied; however, rotavirus cell release is still poorly understood. Specifically, the mechanism by which rotaviruses leave the cell before cell lysis is not known. Previous works have found rotavirus proteins and viral particles associated with extracellular vesicles secreted by cells. These vesicles have been shown to contain markers of exosomes; however, in a recent work they presented characteristics more typical of microparticles, and they were associated with an increase in the infectivity of the virus. In this work, we purified different types of vesicles from rotavirus-infected cells. We analyzed the association of virus with these vesicles and their possible role in promotion of rotavirus infection. We confirmed a non-lytic rotavirus release from the two cell lines tested, and observed a notable stimulation of vesicle secretion following rotavirus infection. A fraction of the secreted viral particles present in the cell supernatant was protected from protease treatment, possibly through its association with membranous vesicles; the more pronounced association of the virus was with fractions corresponding to cell membrane generated microvesicles. Using electron microscopy, we found different size vesicles with particles resembling rotaviruses associated from both- the outside and the inside. The viral particles inside the vesicles were refractory to neutralization with a potent rotavirus neutralizing monoclonal antibody, and were able to infect cells even without trypsin activation. The association of rotavirus particles with extracellular vesicles suggests these might have a role in virus spread.
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Affiliation(s)
- Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (A.P.-D.); (S.L.); (C.F.A.)
- Correspondence: ; Tel.: +52-777-3291612
| | - Arianna Pérez-Delgado
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (A.P.-D.); (S.L.); (C.F.A.)
| | - Iván R. Quevedo
- Departamento de Ingeniería Química Industrial y de Alimentos, Universidad Iberoamericana, Ciudad de México CP 01219, Mexico;
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (A.P.-D.); (S.L.); (C.F.A.)
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico; (A.P.-D.); (S.L.); (C.F.A.)
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Martínez JL, Arias CF. Role of the Guanine Nucleotide Exchange Factor GBF1 in the Replication of RNA Viruses. Viruses 2020; 12:E682. [PMID: 32599855 PMCID: PMC7354614 DOI: 10.3390/v12060682] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022] Open
Abstract
The guanine nucleotide exchange factor GBF1 is a well-known factor that can activate different ADP-ribosylation factor (Arf) proteins during the regulation of different cellular vesicular transport processes. In the last decade, it has become increasingly evident that GBF1 can also regulate different steps of the replication cycle of RNA viruses belonging to different virus families. GBF1 has been shown not only to facilitate the intracellular traffic of different viral and cellular elements during infection, but also to modulate the replication of viral RNA, the formation and maturation of viral replication complexes, and the processing of viral proteins through mechanisms that do not depend on its canonical role in intracellular transport. Here, we review the various roles that GBF1 plays during the replication of different RNA viruses.
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Affiliation(s)
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 4510, Morelos, Mexico;
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Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Ahmed AA, Ganesh V, Tamhankar M, Patterson JL, Ndembi N, Mbanya D, Kaptue L, McArthur C, Muñoz-Medina JE, Gonzalez-Bonilla CR, López S, Arias CF, Arevalo S, Miller S, Stone M, Busch M, Hsieh K, Messenger S, Wadford DA, Rodgers M, Cloherty G, Faria NR, Thézé J, Pybus OG, Neto Z, Morais J, Taveira N, Hackett JR, Chiu CY. Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol 2020; 5:525. [PMID: 31965087 PMCID: PMC7608365 DOI: 10.1038/s41564-020-0671-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Asmeeta Achari
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Inês Bártolo
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Shigeo Yagi
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | - Jimmy Kapetshi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Asim A Ahmed
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Vijay Ganesh
- Massachussetts General Hospital, Boston, MA, USA
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Nicaise Ndembi
- Institute for Human Virology Nigeria, Abuja, Nigeria.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dora Mbanya
- Universite de Yaoundé I, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | | | | | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Kristina Hsieh
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Sharon Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Zoraima Neto
- Angolan National Institute of Health Research, Luanda, Angola
| | - Joana Morais
- Angolan National Institute of Health Research, Luanda, Angola
| | - Nuno Taveira
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.,Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Ahmed AA, Ganesh V, Tamhankar M, Patterson JL, Ndembi N, Mbanya D, Kaptue L, McArthur C, Muñoz-Medina JE, Gonzalez-Bonilla CR, López S, Arias CF, Arevalo S, Miller S, Stone M, Busch M, Hsieh K, Messenger S, Wadford DA, Rodgers M, Cloherty G, Faria NR, Thézé J, Pybus OG, Neto Z, Morais J, Taveira N, R Hackett J, Chiu CY. Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol 2020; 5:443-454. [PMID: 31932713 PMCID: PMC7047537 DOI: 10.1038/s41564-019-0637-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 11/08/2019] [Indexed: 12/27/2022]
Abstract
Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of viral outbreaks. An additional target enrichment step is generally needed for high-sensitivity pathogen identification in low-titre infections, yet available methods using PCR or capture probes can be limited by high cost, narrow scope of detection, lengthy protocols and/or cross-contamination. Here, we developed metagenomic sequencing with spiked primer enrichment (MSSPE), a method for enriching targeted RNA viral sequences while simultaneously retaining metagenomic sensitivity for other pathogens. We evaluated MSSPE for 14 different viruses, yielding a median tenfold enrichment and mean 47% (±16%) increase in the breadth of genome coverage over mNGS alone. Virus detection using MSSPE arboviral or haemorrhagic fever viral panels was comparable in sensitivity to specific PCR, demonstrating 95% accuracy for the detection of Zika, Ebola, dengue, chikungunya and yellow fever viruses in plasma samples from infected patients. Notably, sequences from re-emerging and/or co-infecting viruses that have not been specifically targeted a priori, including Powassan and Usutu, were successfully enriched using MSSPE. MSSPE is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making this method directly applicable for diagnostic laboratory and field use. This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Asmeeta Achari
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Inês Bártolo
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Shigeo Yagi
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | - Jimmy Kapetshi
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | | | - Asim A Ahmed
- Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Vijay Ganesh
- Massachussetts General Hospital, Boston, MA, USA
| | - Manasi Tamhankar
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Nicaise Ndembi
- Institute for Human Virology Nigeria, Abuja, Nigeria.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dora Mbanya
- Universite de Yaoundé I, Yaoundé, Cameroon.,University of Bamenda, Bamenda, Cameroon
| | | | | | | | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Kristina Hsieh
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Sharon Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA
| | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Zoraima Neto
- Angolan National Institute of Health Research, Luanda, Angola
| | - Joana Morais
- Angolan National Institute of Health Research, Luanda, Angola
| | - Nuno Taveira
- Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal.,Instituto Universitário Egas Moniz (IUEM), Monte de Caparica, Portugal
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. .,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA. .,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA.
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Sandoval-Jaime C, Guzmán-Ruiz L, López S, Arias CF. Development of a novel DNA based reverse genetics system for classic human astroviruses. Virology 2019; 535:130-135. [DOI: 10.1016/j.virol.2019.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 01/05/2023]
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Garcés Suárez Y, Martínez JL, Torres Hernández D, Hernández HO, Pérez-Delgado A, Méndez M, Wood CD, Rendon-Mancha JM, Silva-Ayala D, López S, Guerrero A, Arias CF. Nanoscale organization of rotavirus replication machineries. eLife 2019; 8:e42906. [PMID: 31343403 PMCID: PMC6692110 DOI: 10.7554/elife.42906] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
Abstract
Rotavirus genome replication and assembly take place in cytoplasmic electron dense inclusions termed viroplasms (VPs). Previous conventional optical microscopy studies observing the intracellular distribution of rotavirus proteins and their organization in VPs have lacked molecular-scale spatial resolution, due to inherent spatial resolution constraints. In this work we employed super-resolution microscopy to reveal the nanometric-scale organization of VPs formed during rotavirus infection, and quantitatively describe the structural organization of seven viral proteins within and around the VPs. The observed viral components are spatially organized as five concentric layers, in which NSP5 localizes at the center of the VPs, surrounded by a layer of NSP2 and NSP4 proteins, followed by an intermediate zone comprised of the VP1, VP2, VP6. In the outermost zone, we observed a ring of VP4 and finally a layer of VP7. These findings show that rotavirus VPs are highly organized organelles.
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Affiliation(s)
- Yasel Garcés Suárez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Jose L Martínez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - David Torres Hernández
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Laboratorio Nacional de Microscopía Avanzada, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Haydee Olinca Hernández
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Laboratorio Nacional de Microscopía Avanzada, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Arianna Pérez-Delgado
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Mayra Méndez
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y AplicadasUniversidad Autónoma del Estado de MorelosCuernavacaMexico
| | - Christopher D Wood
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Laboratorio Nacional de Microscopía Avanzada, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Juan Manuel Rendon-Mancha
- Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y AplicadasUniversidad Autónoma del Estado de MorelosCuernavacaMexico
| | - Daniela Silva-Ayala
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Adán Guerrero
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Laboratorio Nacional de Microscopía Avanzada, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
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Meyer L, López T, Espinosa R, Arias CF, Vollmers C, DuBois RM. A simplified workflow for monoclonal antibody sequencing. PLoS One 2019; 14:e0218717. [PMID: 31233538 PMCID: PMC6590890 DOI: 10.1371/journal.pone.0218717] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/07/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of antibody variable regions makes cDNA sequencing challenging, and conventional monoclonal antibody cDNA amplification requires the use of degenerate primers. Here, we describe a simplified workflow for amplification of IgG antibody variable regions from hybridoma RNA by a specialized RT-PCR followed by Sanger sequencing. We perform three separate reactions for each hybridoma: one each for kappa, lambda, and heavy chain transcripts. We prime reverse transcription with a primer specific to the respective constant region and use a template-switch oligonucleotide, which creates a custom sequence at the 5’ end of the antibody cDNA. This template-switching circumvents the issue of low sequence homology and the need for degenerate primers. Instead, subsequent PCR amplification of the antibody cDNA molecules requires only two primers: one primer specific for the template-switch oligonucleotide sequence and a nested primer to the respective constant region. We successfully sequenced the variable regions of five mouse monoclonal IgG antibodies using this method, which enabled us to design chimeric mouse/human antibody expression plasmids for recombinant antibody production in mammalian cell culture expression systems. All five recombinant antibodies bind their respective antigens with high affinity, confirming that the amino acid sequences determined by our method are correct and demonstrating the high success rate of our method. Furthermore, we also designed RT-PCR primers and amplified the variable regions from RNA of cells transfected with chimeric mouse/human antibody expression plasmids, showing that our approach is also applicable to IgG antibodies of human origin. Our monoclonal antibody sequencing method is highly accurate, user-friendly, and very cost-effective.
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Affiliation(s)
- Lena Meyer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rafaela Espinosa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (RMD); (CV)
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (RMD); (CV)
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Oceguera A, Peralta AV, Martínez-Delgado G, Arias CF, López S. Rotavirus RNAs sponge host cell RNA binding proteins and interfere with their subcellular localization. Virology 2018; 525:96-105. [PMID: 30253276 DOI: 10.1016/j.virol.2018.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/13/2018] [Accepted: 09/17/2018] [Indexed: 10/28/2022]
Abstract
Cellular mRNAs cycle between translating and non-translating pools, polysomes compose the translating pool, while RNA granules contain translationally-silenced mRNAs, where the RNAs are either stored in stress granules, or accumulate in processing bodies (PBs) or GW-bodies, which have an important role in RNA degradation. Viruses have developed measures to prevent the deleterious effects of these structures during their replication. Rotavirus, the most common agent of viral gastroenteritis, is capable of establishing a successful infection by counteracting several of the antiviral responses of its host. Here, we describe that in rotavirus-infected cells the distribution of several RNA binding proteins is changed causing the disaggregation of PBs, the relocalization of GW-body proteins, and the cytoplasmic accumulation of HuR, a predominantly nuclear protein. We show that this redistribution of proteins is more likely caused by the accumulation of viral RNA in the cytoplasm of infected-cells, where it might be acting as an RBP sponge.
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Affiliation(s)
- Alfonso Oceguera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Andrea V Peralta
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Gustavo Martínez-Delgado
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico.
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41
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Salgado‐Roa FC, Pardo‐Diaz C, Lasso E, Arias CF, Solferini VN, Salazar C. Gene flow and Andean uplift shape the diversification of Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America. Ecol Evol 2018; 8:7131-7142. [PMID: 30073072 PMCID: PMC6065347 DOI: 10.1002/ece3.4237] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 01/08/2023] Open
Abstract
The Andean uplift has played a major role in shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here, we examined the phylogeography of the widespread color polymorphic spider Gasteracantha cancriformis to evaluate the effect of the northern Andean uplift on its divergence and assess whether its diversification occurred in the presence of gene flow. We inferred phylogenetic relationships and divergence times in G. cancriformis using mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence, and population structure were quantified. We also compared multiple demographic scenarios for this species using a model-based approach (phrapl) to determine divergence with or without gene flow. At last, we evaluated the association between genetic variation and color polymorphism. Both nuclear and mitochondrial data supported two well-differentiated clades, which correspond to populations occurring on opposite sides of the Eastern cordillera of the Colombian Andes. The final uplift of this cordillera was identified as the most likely force that shaped the diversification of G. cancriformis in northern South America, resulting in a cis- and trans-Andean phylogeographic structure for the species. We also found shared genetic variation between the cis- and trans-Andean clades, which is better explained by a scenario of historical divergence in the face of gene flow. This has been likely facilitated by the presence of low-elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example in which the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.
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Affiliation(s)
- Fabian C. Salgado‐Roa
- Programa de BiologíaFacultad de Ciencias Naturales y MatemáticasUniversidad del RosarioBogotáColombia
- Departamento de Ciencias BiológicasUniversidad de los AndesBogotáColombia
| | - Carolina Pardo‐Diaz
- Programa de BiologíaFacultad de Ciencias Naturales y MatemáticasUniversidad del RosarioBogotáColombia
| | - Eloisa Lasso
- Departamento de Ciencias BiológicasUniversidad de los AndesBogotáColombia
- Smithsonian Tropical Research InstituteAncónPanamá
| | | | - Vera Nisaka Solferini
- Department of Genetics, Evolution and BioagentsInstitute of BiologyUniversity of CampinasCampinasSao PauloBrazil
| | - Camilo Salazar
- Programa de BiologíaFacultad de Ciencias Naturales y MatemáticasUniversidad del RosarioBogotáColombia
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42
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Thézé J, Li T, du Plessis L, Bouquet J, Kraemer MUG, Somasekar S, Yu G, de Cesare M, Balmaseda A, Kuan G, Harris E, Wu CH, Ansari MA, Bowden R, Faria NR, Yagi S, Messenger S, Brooks T, Stone M, Bloch EM, Busch M, Muñoz-Medina JE, González-Bonilla CR, Wolinsky S, López S, Arias CF, Bonsall D, Chiu CY, Pybus OG. Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico. Cell Host Microbe 2018; 23:855-864.e7. [PMID: 29805095 PMCID: PMC6006413 DOI: 10.1016/j.chom.2018.04.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/27/2018] [Accepted: 04/26/2018] [Indexed: 02/06/2023]
Abstract
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures.
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Affiliation(s)
- Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Tony Li
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Jerome Bouquet
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK; Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Harvard University, Boston, MA, USA
| | - Sneha Somasekar
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Mariateresa de Cesare
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Angel Balmaseda
- Laboratory Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - M Azim Ansari
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rory Bowden
- Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
| | - Shigeo Yagi
- California Department of Public Health, Richmond, CA, USA
| | | | - Trevor Brooks
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medcine, Baltimore, MD, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA, USA
| | - José E Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Cesar R González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - David Bonsall
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA; Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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43
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Aguilar-Hernández N, López S, Arias CF. Minimal capsid composition of infectious human astrovirus. Virology 2018; 521:58-61. [PMID: 29883775 DOI: 10.1016/j.virol.2018.05.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/30/2022]
Abstract
Human astrovirus is an important etiological agent of acute gastroenteritis in young children. Despite advances in the characterization of the structure of the virion by cryo-electron microscopy and of capsid proteins by x-ray crystallography, the definition of the minimal polypeptide composition of infectious virus particles has been elusive. In this work we show that mature infectious particles are composed by only two proteins; VP34 that forms the core domain of the virus, and VP27 that constitutes the 30 dimeric spikes present on the virus surface. Our results also indicate that during the transition of immature (90 spikes) to mature (30 spikes) virus particles, that occur during trypsin activation, the viral protein VP25, that most likely forms the 60 spikes that are lost during maturation, detaches from the virus particle. This information is relevant to better understand the biology of virus entry and also for the efficient development of subunit vaccines.
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Affiliation(s)
- Nayeli Aguilar-Hernández
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Carlos F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico.
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44
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Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, Runge AK, Thézé J, Streicker D, Frank HK, Loza-Rubio E, Liu S, Ryder OA, Samaniego Castruita JA, Katzourakis A, Pacheco G, Taboada B, Löber U, Pybus OG, Li Y, Rojas-Anaya E, Bohmann K, Carmona Baez A, Arias CF, Liu S, Greenwood AD, Bertelsen MF, White NE, Bunce M, Zhang G, Sicheritz-Pontén T, Gilbert MPT. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nat Ecol Evol 2018; 2:659-668. [PMID: 29459707 PMCID: PMC5868727 DOI: 10.1038/s41559-018-0476-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/11/2018] [Indexed: 11/21/2022]
Abstract
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.
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Affiliation(s)
- M Lisandra Zepeda Mendoza
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Zijun Xiong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Marina Escalera-Zamudio
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Anne Kathrine Runge
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Daniel Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine & MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Hannah K Frank
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Ciudad de México, Mexico
| | - Shengmao Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - George Pacheco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | | | - Yang Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Edith Rojas-Anaya
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Ciudad de México, Mexico
| | - Kristine Bohmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aldo Carmona Baez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Undergraduate Program for Genomic Sciences, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nicole E White
- Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, Perth, Australia
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Michael Bunce
- Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, Perth, Australia
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - M P Thomas Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia.
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway.
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45
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Escalera-Zamudio M, Taboada B, Rojas-Anaya E, Löber U, Loza-Rubio E, Arias CF, Greenwood AD. Viral Communities Among Sympatric Vampire Bats and Cattle. Ecohealth 2018; 15:132-142. [PMID: 29164470 DOI: 10.1007/s10393-017-1297-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Vampire bats are the only mammals known to feed exclusively on blood from other animals, often from domestic cattle. We tested the hypothesis that the adaptation of vampire bats to hematophagy would have resulted in shared viral communities among vampire bats and cattle, as a direct result of historic spillover events occurring due to hematophagy. We analyzed the presence of different viruses in sample populations of sympatric bat and prey populations and searched for shared viruses between taxa. A limited number of DNA viral groups were detected within each species. However, there was no evidence for a shared viral community among the vampire bat and cattle populations tested.
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Affiliation(s)
- Marina Escalera-Zamudio
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Parks Rd, Oxford, OX1 3SY, UK.
| | - Blanca Taboada
- Departamento de Genetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Edith Rojas-Anaya
- Centro Nacional de Investigacion Disciplinaria en Microbiologia Animal CENID-INIFAP, Mexico City, Mexico
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigacion Disciplinaria en Microbiologia Animal CENID-INIFAP, Mexico City, Mexico
| | - Carlos F Arias
- Departamento de Genetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
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46
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Díaz-Salinas MA, Casorla LA, López T, López S, Arias CF. Most rotavirus strains require the cation-independent mannose-6-phosphate receptor, sortilin-1, and cathepsins to enter cells. Virus Res 2017; 245:44-51. [PMID: 29275103 PMCID: PMC7173016 DOI: 10.1016/j.virusres.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Rotaviruses require the TGN to LE transporter CI-M6PR for cell entry. Sortilin-1 was identified as a cell factor involved in rotavirus replication. Rotaviruses require cathepsins also to enter Caco-2 cells.
Cathepsins, endosomal acid proteases, are transported from the trans-Golgi network to late endosomes by the mannose-6-phosphate receptor (M6PR). We have previously demonstrated that some rotavirus strains, like UK, Wa, WI61, DS-1, and YM, require the cation-dependent (CD-) M6PR and cathepsins to enter from late endosomes to the cytoplasm in MA104 cells, while other strains, like the simian strain RRV, which enter cells from maturing endosomes, do not. However, the role of other trans-Golgi network-late endosome transporters, such as the cation-independent (CI-) M6PR and sortillin-1, has not been evaluated. In this work, we found that several rotavirus strains that require the CD-M6PR for cell entry are also dependent on CI-M6PR and sortilin-1. Furthermore, we showed that the infectivity of all these rotavirus strains also requires cathepsins to enter not only MA104 cells, but also human intestinal Caco-2 cells. This study identifies sortilin-1 as a novel cell factor necessary for the infectivity of a virus; in addition, our results strongly suggest that cathepsins could be common cell factors needed for the infectivity of most rotavirus strains.
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Affiliation(s)
- Marco A Díaz-Salinas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Luis A Casorla
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico.
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47
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48
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Enciso-Romero J, Pardo-Díaz C, Martin SH, Arias CF, Linares M, McMillan WO, Jiggins CD, Salazar C. Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies. Mol Ecol 2017; 26:5160-5172. [PMID: 28777894 DOI: 10.1111/mec.14277] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 12/25/2022]
Abstract
Understanding the genetic basis of phenotypic variation and the mechanisms involved in the evolution of adaptive novelty, especially in adaptive radiations, is a major goal in evolutionary biology. Here, we used whole-genome sequence data to investigate the origin of the yellow hindwing bar in the Heliconius cydno radiation. We found modular variation associated with hindwing phenotype in two narrow noncoding regions upstream and downstream of the cortex gene, which was recently identified as a pigmentation pattern controller in multiple species of Heliconius. Genetic variation at each of these modules suggests an independent control of the dorsal and ventral hindwing patterning, with the upstream module associated with the ventral phenotype and the downstream module with the dorsal one. Furthermore, we detected introgression between H. cydno and its closely related species Heliconius melpomene in these modules, likely allowing both species to participate in novel mimicry rings. In sum, our findings support the role of regulatory modularity coupled with adaptive introgression as an elegant mechanism by which novel phenotypic combinations can evolve and fuel an adaptive radiation.
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Affiliation(s)
- Juan Enciso-Romero
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | - Carolina Pardo-Díaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Carlos F Arias
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia.,Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - Mauricio Linares
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
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49
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Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 2017; 546:406-410. [PMID: 28538727 DOI: 10.1038/nature22401] [Citation(s) in RCA: 377] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/02/2017] [Indexed: 12/21/2022]
Abstract
Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 2016) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 2016). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.
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Affiliation(s)
- N R Faria
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK.,Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil
| | - J Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - I M Claro
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - J Thézé
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - J G de Jesus
- Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - M Giovanetti
- Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil.,University of Rome Tor Vergata, Rome, Italy
| | - M U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK.,Harvard Medical School, Boston, Massachusetts, USA.,Boston Children's Hospital, Boston, Massachusetts, USA
| | - S C Hill
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - A Black
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - A C da Costa
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - L C Franco
- Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil
| | - S P Silva
- Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil
| | - C-H Wu
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - J Raghwani
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - S Cauchemez
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, URA3012, Paris, France
| | - L du Plessis
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - M P Verotti
- Coordenação dos Laboratórios de Saúde (CGLAB/DEVIT/SVS), Ministry of Health, Brasília, Brazil
| | - W K de Oliveira
- Coordenação Geral de Vigilância e Resposta às Emergências em Saúde Pública (CGVR/DEVIT), Ministry of Health, Brasília, Brazil.,Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - E H Carmo
- Departamento de Vigilância das Doenças Transmissíveis, Ministry of Health, Brasilia, Brazil
| | - G E Coelho
- Coordenação Geral dos Programas de Controle e Prevenção da Malária e das Doenças Transmitidas pelo Aedes, Ministry of Health, Brasília, Brazil.,Pan American Health Organization (PAHO), Buenos Aires, Argentina
| | - A C F S Santelli
- Coordenação Geral dos Programas de Controle e Prevenção da Malária e das Doenças Transmitidas pelo Aedes, Ministry of Health, Brasília, Brazil.,Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - L C Vinhal
- Coordenação Geral dos Programas de Controle e Prevenção da Malária e das Doenças Transmitidas pelo Aedes, Ministry of Health, Brasília, Brazil
| | - C M Henriques
- Departamento de Vigilância das Doenças Transmissíveis, Ministry of Health, Brasilia, Brazil
| | - J T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - M Loose
- University of Nottingham, Nottingham, UK
| | - K G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - N D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - S Somasekar
- Departments of Laboratory Medicine and Medicine &Infectious Diseases, University of California, San Francisco, California, USA
| | - C Y Chiu
- Departments of Laboratory Medicine and Medicine &Infectious Diseases, University of California, San Francisco, California, USA
| | - J E Muñoz-Medina
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - C R Gonzalez-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - C F Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - A O Chieppe
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil
| | - S F Aguiar
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil
| | - C A Fernandes
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil
| | - P S Lemos
- Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil
| | - B L S Nascimento
- Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil
| | - H A O Monteiro
- Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil
| | - I C Siqueira
- Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - M G de Queiroz
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Norte, Natal, Brazil
| | - T R de Souza
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Norte, Natal, Brazil.,Universidade Potiguar do Rio Grande do Norte, Natal, Brazil
| | - J F Bezerra
- Laboratório Central de Saúde Pública do Estado do Rio Grande do Norte, Natal, Brazil.,Faculdade Natalense de Ensino e Cultura, Rio Grande do Norte, Natal, Brazil
| | - M R Lemos
- Laboratório Central de Saúde Pública do Estado da Paraíba, João Pessoa, Brazil
| | - G F Pereira
- Laboratório Central de Saúde Pública do Estado da Paraíba, João Pessoa, Brazil
| | - D Loudal
- Laboratório Central de Saúde Pública do Estado da Paraíba, João Pessoa, Brazil
| | - L C Moura
- Laboratório Central de Saúde Pública do Estado da Paraíba, João Pessoa, Brazil
| | - R Dhalia
- Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil
| | - R F França
- Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil
| | - T Magalhães
- Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil.,Department of Microbiology, Immunology &Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - E T Marques
- Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil
| | - T Jaenisch
- Section Clinical Tropical Medicine, Department for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - G L Wallau
- Fundação Oswaldo Cruz (FIOCRUZ), Recife, Pernambuco, Brazil
| | - M C de Lima
- Laboratório Central de Saúde Pública do Estado de Alagoas, Maceió, Brazil
| | - V Nascimento
- Laboratório Central de Saúde Pública do Estado de Alagoas, Maceió, Brazil
| | - E M de Cerqueira
- Laboratório Central de Saúde Pública do Estado de Alagoas, Maceió, Brazil
| | - M M de Lima
- Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - D L Mascarenhas
- Secretaria de Saúde de Feira de Santana, Feira de Santana, Bahia, Brazil
| | | | - A S Levin
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - T R Tozetto-Mendoza
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - S N Fonseca
- Hospital São Francisco, Ribeirão Preto, Brazil
| | - M C Mendes-Correa
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | - F P Milagres
- Universidade Federal do Tocantins, Palmas, Brazil
| | - A Segurado
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | | | - A Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.,Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - T Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - M R T Nunes
- Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil.,Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - E C Sabino
- Department of Infectious Disease, School of Medicine &Institute of Tropical Medicine, University of São Paulo, São Paulo, Brazil
| | | | - N J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK.,Metabiota, San Francisco, California 94104, USA
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Arias CF, Giraldo N, McMillan WO, Lamas G, Jiggins CD, Salazar C. A new subspecies in a Heliconius butterfly adaptive radiation (Lepidoptera: Nymphalidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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