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Wang T, Yu ZG, Li J. CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model. Front Microbiol 2024; 15:1339156. [PMID: 38572227 PMCID: PMC10987876 DOI: 10.3389/fmicb.2024.1339156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 04/05/2024] Open
Abstract
Traditional alignment-based methods meet serious challenges in genome sequence comparison and phylogeny reconstruction due to their high computational complexity. Here, we propose a new alignment-free method to analyze the phylogenetic relationships (classification) among species. In our method, the dynamical language (DL) model and the chaos game representation (CGR) method are used to characterize the frequency information and the context information of k-mers in a sequence, respectively. Then for each DNA sequence or protein sequence in a dataset, our method converts the sequence into a feature vector that represents the sequence information based on CGR weighted by the DL model to infer phylogenetic relationships. We name our method CGRWDL. Its performance was tested on both DNA and protein sequences of 8 datasets of viruses to construct the phylogenetic trees. We compared the Robinson-Foulds (RF) distance between the phylogenetic tree constructed by CGRWDL and the reference tree by other advanced methods for each dataset. The results show that the phylogenetic trees constructed by CGRWDL can accurately classify the viruses, and the RF scores between the trees and the reference trees are smaller than that with other methods.
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Affiliation(s)
- Ting Wang
- National Center for Applied Mathematics in Hunan, Xiangtan University, Xiangtan, Hunan, China
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, China
| | - Zu-Guo Yu
- National Center for Applied Mathematics in Hunan, Xiangtan University, Xiangtan, Hunan, China
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan, Hunan, China
| | - Jinyan Li
- School of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, China
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Caraballo DA, Sabio MS, Colombo VC, Piccirilli MG, Vico L, Hirmas Riade SM, Campos J, Martínez G, Beltrán F, Baumeister E, Cisterna DM. The Role of Molossidae and Vespertilionidae in Shaping the Diversity of Alphacoronaviruses in the Americas. Microbiol Spectr 2022; 10:e0314322. [PMID: 36222689 PMCID: PMC9769993 DOI: 10.1128/spectrum.03143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/20/2022] [Indexed: 01/10/2023] Open
Abstract
Bats are reservoirs of diverse coronaviruses (CoVs), including progenitors of severe acute respiratory syndrome CoV (SARS-CoV) and SARS-CoV-2. In the Americas, there is a contrast between alphacoronaviruses (alphaCoVs) and betaCoVs: while cospeciation prevails in the latter, alphaCoV evolution is dominated by deep and recent host switches. AlphaCoV lineages are maintained by two different bat family groups, Phyllostomidae and Vespertilionidae plus Molossidae. In this study, we used a Bayesian framework to analyze the process of diversification of the lineages maintained by Molossidae and Vespertilionidae, adding novel CoV sequences from Argentina. We provide evidence that the observed CoV diversity in these two bat families is shaped by their geographic distribution and that CoVs exhibit clustering at the level of bat genera. We discuss the causes of the cocirculation of two independent clades in Molossus and Tadarida as well as the role of Myotis as the ancestral host and a major evolutionary reservoir of alphaCoVs across the continent. Although more CoV sampling efforts are needed, these findings contribute to a better knowledge of the diversity of alphaCoVs and the links between bat host species. IMPORTANCE Bats harbor the largest diversity of coronaviruses among mammals. In the Americas, seven alphacoronavirus lineages circulate among bats. Three of these lineages are shared by members of two bat families: Vespertilionidae and Molossidae. Uncovering the relationships between these coronaviruses can help us to understand patterns of cross-species transmission and, ultimately, which hosts are more likely to be involved in spillover events. We found that two different lineages cocirculate among the bat genera Molossus and Tadarida, which share roosts and have common viral variants. The bat genus Myotis functions as a reservoir of coronavirus diversity and, as such, is a key host. Although there were some spillovers recorded, there is a strong host association, showing that once a successful host jump takes place, it is transmitted onward to members of the same bat genus.
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Affiliation(s)
- Diego A. Caraballo
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Ciudad Universitaria-Pabellón II, Ciudad Autónoma de Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - María S. Sabio
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Valeria C. Colombo
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - María Guadalupe Piccirilli
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lorena Vico
- Departamento de Zoonosis Urbanas, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Stella Maris Hirmas Riade
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Josefina Campos
- Unidad de Genómica y Bioinformática, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gustavo Martínez
- Departamento de Zoonosis Urbanas, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Fernando Beltrán
- Instituto de Zoonosis Dr. Luis Pasteur, Ciudad Autónoma de Buenos Aires, Argentina
| | - Elsa Baumeister
- Servicio de Virosis Respiratorias, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel M. Cisterna
- Servicio de Neurovirosis, Instituto Nacional de Enfermedades Infecciosas, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS), Dr. Carlos G. Malbrán, Ciudad Autónoma de Buenos Aires, Argentina
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Non-coding RNA in SARS-CoV-2: Progress toward therapeutic significance. Int J Biol Macromol 2022; 222:1538-1550. [PMID: 36152703 PMCID: PMC9492401 DOI: 10.1016/j.ijbiomac.2022.09.105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 12/18/2022]
Abstract
The recently developed pathogenic virus, SARS-CoV-2, was found in the Hubei Province, China. Giving rise to a broad spectrum of symptoms, SARS-CoV-2 rapidly spread across the globe, causing multi-systemic and dangerous complications, with death in extreme cases. Thereby, the number of research cases increases every day on preventing infection and treating its resulting damage. Accumulating evidence suggests noncoding RNAs (ncRNAs) are necessary for modifying virus infection and antiviral immune reaction, along with biological processes regulating SARS-CoV-2 and subsequent disease states. Therefore, understanding these mechanisms might provide a further understanding of the pathogenesis and feasible therapy alternatives against SARS-CoV2. Consequently, the molecular biology of SARS-CoV-2, ncRNA's role in its infection, and various RNA therapy tactics against the virus have been presented in this review section.
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Caraballo DA. Cross-Species Transmission of Bat Coronaviruses in the Americas: Contrasting Patterns between Alphacoronavirus and Betacoronavirus. Microbiol Spectr 2022; 10:e0141122. [PMID: 35770987 PMCID: PMC9431099 DOI: 10.1128/spectrum.01411-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 01/09/2023] Open
Abstract
Bats harbor the largest number of coronavirus (CoV) species among mammals, serving as major reservoirs of alphaCoVs and betaCoVs, which can jump between bat species or to different mammalian hosts, including humans. Bat-CoV diversity is correlated with host taxonomic diversity, with the highest number of CoV species found in areas with the highest levels of bat species richness. Although the Americas harbor a unique and distinctive CoV diversity, no cross-species transmission (CST) or phylogeographic analysis has yet been performed. This study analyzes a large sequence data set from across the Americas through a Bayesian framework to understand how codivergence and cross-species transmission have shaped long-term bat-CoV evolution and ultimately identify bat hosts and regions where the risk of CST is the highest. Substantial levels of CST were found only among alphaCoVs. In contrast, cospeciation prevailed along the evolution of betaCoVs. Brazil is the center of diversification for both alpha and betaCoVs, with the highest levels of bat species richness. The bat family Phyllostomidae has played a key role in the evolution of American bat-CoVs, supported by the highest values of host transition rates. Although the conclusions drawn from this study are supported by biological/ecological evidence, it is likely that novel lineages will be discovered, which could also reveal undetected CSTs given that sequences are available from 11 of the 35 countries encompassing the Americas. The findings of this study can be useful for conducting targeted discovery of bat-CoVs in the region, especially in countries of the Americas with no reported sequences. IMPORTANCE Coronaviruses (CoVs) have a strong zoonotic potential due to their high rates of evolvability and their capacity for overcoming host-specific barriers. Bats harbor the largest number of CoV species among mammals, with the highest CoV diversity found in areas with the highest levels of bat species richness. Understanding their origin and patterns of cross-species transmission is crucial for pandemic preparedness. This study aims to understand how bat-CoVs diversify in the Americas, circulate among and transmit between bat families and genera, and ultimately identify bat hosts and regions where the risk of CoV spillover is the highest.
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Affiliation(s)
- Diego A. Caraballo
- CONICET-Universidad de Buenos Aires, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Ciudad Universitaria-Pabellón II, Buenos Aires, Argentina
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
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