Integrating full and partial genome sequences to decipher the global spread of canine rabies virus
Abstract Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-39847-x |
| _version_ | 1797774078670536704 |
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| author | Andrew Holtz Guy Baele Hervé Bourhy Anna Zhukova |
| author_facet | Andrew Holtz Guy Baele Hervé Bourhy Anna Zhukova |
| author_sort | Andrew Holtz |
| collection | DOAJ |
| description | Abstract Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to investigate historical pathogen spread between countries. Its application to rabies virus (RABV) yields precise dating and confident estimates of its geographic dispersal. By using full genomes and partial sequences, we reduce both geographic and genetic biases that often hinder studies that focus on specific genes. Our pipeline reveals an emergence of the present canine-mediated RABV between years 1301 and 1403 and reveals regional introductions over a 700-year period. This geographic reconstruction enables us to locate episodes of human-mediated introductions of RABV and examine the role that European colonization played in its spread. Our approach enables phylogeographic analysis of large and genetically diverse data sets for many viral pathogens. |
| first_indexed | 2024-03-12T22:14:48Z |
| format | Article |
| id | doaj.art-493e5a0ef76b47e39a8b3775771d99cf |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-12T22:14:48Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-493e5a0ef76b47e39a8b3775771d99cf2023-07-23T11:20:16ZengNature PortfolioNature Communications2041-17232023-07-0114111310.1038/s41467-023-39847-xIntegrating full and partial genome sequences to decipher the global spread of canine rabies virusAndrew Holtz0Guy Baele1Hervé Bourhy2Anna Zhukova3Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology UnitDepartment of Microbiology, Immunology and Transplantation, Rega InstituteInstitut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology UnitInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubAbstract Despite the rapid growth in viral genome sequencing, statistical methods face challenges in handling historical viral endemic diseases with large amounts of underutilized partial sequence data. We propose a phylogenetic pipeline that harnesses both full and partial viral genome sequences to investigate historical pathogen spread between countries. Its application to rabies virus (RABV) yields precise dating and confident estimates of its geographic dispersal. By using full genomes and partial sequences, we reduce both geographic and genetic biases that often hinder studies that focus on specific genes. Our pipeline reveals an emergence of the present canine-mediated RABV between years 1301 and 1403 and reveals regional introductions over a 700-year period. This geographic reconstruction enables us to locate episodes of human-mediated introductions of RABV and examine the role that European colonization played in its spread. Our approach enables phylogeographic analysis of large and genetically diverse data sets for many viral pathogens.https://doi.org/10.1038/s41467-023-39847-x |
| spellingShingle | Andrew Holtz Guy Baele Hervé Bourhy Anna Zhukova Integrating full and partial genome sequences to decipher the global spread of canine rabies virus Nature Communications |
| title | Integrating full and partial genome sequences to decipher the global spread of canine rabies virus |
| title_full | Integrating full and partial genome sequences to decipher the global spread of canine rabies virus |
| title_fullStr | Integrating full and partial genome sequences to decipher the global spread of canine rabies virus |
| title_full_unstemmed | Integrating full and partial genome sequences to decipher the global spread of canine rabies virus |
| title_short | Integrating full and partial genome sequences to decipher the global spread of canine rabies virus |
| title_sort | integrating full and partial genome sequences to decipher the global spread of canine rabies virus |
| url | https://doi.org/10.1038/s41467-023-39847-x |
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