Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources
Due to the necessity to control human-to-human spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the overwhelming majority of the generated data on this virus was solely related to the genomic characteristics of strains infecting humans; conversely, this work aimed to recover a...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-06-01
|
| Series: | One Health |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352771421001531 |
| _version_ | 1818251116777832448 |
|---|---|
| author | Marina Muñoz Luz Helena Patiño Nathalia Ballesteros Sergio Castañeda Nicolás Luna Lourdes Delgado Carlos Hernandez-Pereira Maryia V. Shaban Shirly Alexandra Muñoz Alberto Paniz-Mondolfi Juan David Ramírez |
| author_facet | Marina Muñoz Luz Helena Patiño Nathalia Ballesteros Sergio Castañeda Nicolás Luna Lourdes Delgado Carlos Hernandez-Pereira Maryia V. Shaban Shirly Alexandra Muñoz Alberto Paniz-Mondolfi Juan David Ramírez |
| author_sort | Marina Muñoz |
| collection | DOAJ |
| description | Due to the necessity to control human-to-human spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the overwhelming majority of the generated data on this virus was solely related to the genomic characteristics of strains infecting humans; conversely, this work aimed to recover and analyze the diversity of viral genomes from non-human sources. From a set of 3595 publicly available SARS-CoV-2 genome sequences, 128 lineages were identified in non-human hosts, the majority represented by the variants of concern Delta (n = 1105, 30.7%) and Alpha (n = 466, 12.9%), followed by B.1.1.298 lineage (n = 458, 12.7%). Environment, Neovison vison, Odocoileus virginianus and Felis catus were the non-human sources with the highest number of lineages (14, 12 and 10, respectively). Phylogenomic analyses showed viral clusters from environmental sources, N. vison, O. virginianus, Panthera tigris, and Panthera leo. These clusters were collectively related to human viruses as well as all other non-human sources that were heterogeneously distributed in the phylogenetic tree. Further, the genetic details of viral genomes from bats and pangolins were independently investigated owing to their high divergence, revealing five distinct clusters. Cluster 4 exclusively included bat-sourced genomes and the SARS-CoV-2 reference strain Wuhan-01. In summary, this study identified new genetic landmarks of SARS-CoV-2 evolution. We propose potential interspecies transmission routes of SARS-CoV-2 between animals and humans, which should be considered in order to establish better pathogen surveillance and containment strategies. |
| first_indexed | 2024-12-12T16:03:10Z |
| format | Article |
| id | doaj.art-5cd025d34bdf42d6a0170cee3717a180 |
| institution | Directory Open Access Journal |
| issn | 2352-7714 |
| language | English |
| last_indexed | 2024-12-12T16:03:10Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | One Health |
| spelling | doaj.art-5cd025d34bdf42d6a0170cee3717a1802022-12-22T00:19:22ZengElsevierOne Health2352-77142022-06-0114100363Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sourcesMarina Muñoz0Luz Helena Patiño1Nathalia Ballesteros2Sergio Castañeda3Nicolás Luna4Lourdes Delgado5Carlos Hernandez-Pereira6Maryia V. Shaban7Shirly Alexandra Muñoz8Alberto Paniz-Mondolfi9Juan David Ramírez10Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaCentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, ColombiaInstituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, VenezuelaInstituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, VenezuelaInstituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, VenezuelaCentro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia; Unidad de Salud de Ibagué (USI) E.S.E., Ibagué, ColombiaInstituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela; Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USACentro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA; Corresponding author at: Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.Due to the necessity to control human-to-human spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the overwhelming majority of the generated data on this virus was solely related to the genomic characteristics of strains infecting humans; conversely, this work aimed to recover and analyze the diversity of viral genomes from non-human sources. From a set of 3595 publicly available SARS-CoV-2 genome sequences, 128 lineages were identified in non-human hosts, the majority represented by the variants of concern Delta (n = 1105, 30.7%) and Alpha (n = 466, 12.9%), followed by B.1.1.298 lineage (n = 458, 12.7%). Environment, Neovison vison, Odocoileus virginianus and Felis catus were the non-human sources with the highest number of lineages (14, 12 and 10, respectively). Phylogenomic analyses showed viral clusters from environmental sources, N. vison, O. virginianus, Panthera tigris, and Panthera leo. These clusters were collectively related to human viruses as well as all other non-human sources that were heterogeneously distributed in the phylogenetic tree. Further, the genetic details of viral genomes from bats and pangolins were independently investigated owing to their high divergence, revealing five distinct clusters. Cluster 4 exclusively included bat-sourced genomes and the SARS-CoV-2 reference strain Wuhan-01. In summary, this study identified new genetic landmarks of SARS-CoV-2 evolution. We propose potential interspecies transmission routes of SARS-CoV-2 between animals and humans, which should be considered in order to establish better pathogen surveillance and containment strategies.http://www.sciencedirect.com/science/article/pii/S2352771421001531SARS-CoV-2AnimalsEnvironmentHumansLineagesAlpha variant |
| spellingShingle | Marina Muñoz Luz Helena Patiño Nathalia Ballesteros Sergio Castañeda Nicolás Luna Lourdes Delgado Carlos Hernandez-Pereira Maryia V. Shaban Shirly Alexandra Muñoz Alberto Paniz-Mondolfi Juan David Ramírez Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources One Health SARS-CoV-2 Animals Environment Humans Lineages Alpha variant |
| title | Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources |
| title_full | Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources |
| title_fullStr | Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources |
| title_full_unstemmed | Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources |
| title_short | Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources |
| title_sort | striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non human sources |
| topic | SARS-CoV-2 Animals Environment Humans Lineages Alpha variant |
| url | http://www.sciencedirect.com/science/article/pii/S2352771421001531 |
| work_keys_str_mv | AT marinamunoz strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT luzhelenapatino strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT nathaliaballesteros strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT sergiocastaneda strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT nicolasluna strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT lourdesdelgado strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT carloshernandezpereira strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT maryiavshaban strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT shirlyalexandramunoz strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT albertopanizmondolfi strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources AT juandavidramirez strikinglineagediversityofsevereacuterespiratorysyndromecoronavirus2fromnonhumansources |