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Salazar-Hamm PS, Johnson WL, Nofchissey RA, Salazar JR, Gonzalez P, Goodfellow SM, Dunnum JL, Bradfute SB, Armién B, Cook JA, Domman DB, Dinwiddie DL. Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. PLoS Negl Trop Dis 2024; 18:e0011672. [PMID: 38215158 PMCID: PMC10810438 DOI: 10.1371/journal.pntd.0011672] [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: 10/02/2023] [Revised: 01/25/2024] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Hantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian host populations without causing harm. In Panama, sigmodontine rodents serve as hosts to transmissible hantaviruses. Due to natural and anthropogenic forces, these rodent populations are having increased contact with humans. METHODS We extracted RNA and performed Illumina deep metatranscriptomic sequencing on Orthohantavirus seropositive museum tissues from rodents. We acquired sequence reads mapping to Choclo virus (CHOV, Orthohantavirus chocloense) from heart and kidney tissue of a two-decade old frozen museum sample from a Costa Rican pygmy rice rat (Oligoryzomys costaricensis) collected in Panama. Reads mapped to the CHOV reference were assembled and then validated by visualization of the mapped reads against the assembly. RESULTS We recovered a 91% complete consensus sequence from a reference-guided assembly to CHOV with an average of 16X coverage. The S and M segments used in our phylogenetic analyses were nearly complete (98% and 99%, respectively). There were 1,199 ambiguous base calls of which 93% were present in the L segment. Our assembled genome varied 1.1% from the CHOV reference sequence resulting in eight nonsynonymous mutations. Further analysis of all publicly available partial S segment sequences support a clear relationship between CHOV clinical cases and O. costaricensis acquired strains. CONCLUSIONS Viruses occurring at extremely low abundances can be recovered from deep metatranscriptomics of archival tissues housed in research natural history museum biorepositories. Our efforts resulted in the second CHOV genome publicly available. This genomic data is important for future surveillance and diagnostic tools as well as understanding the evolution and pathogenicity of CHOV.
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Affiliation(s)
- Paris S. Salazar-Hamm
- Clinical and Translational Science Center, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William L. Johnson
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Robert A. Nofchissey
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Jacqueline R. Salazar
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Publio Gonzalez
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Samuel M. Goodfellow
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Jonathan L. Dunnum
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Steven B. Bradfute
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Blas Armién
- Department of Research in Emerging and Zoonotic Infectious Diseases, Gorgas Memorial Institute of Health Studies, Panama City, Panama
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia, Tecnología e Innovacion (SENACYT), Panama City, Panama
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Daryl B. Domman
- Clinical and Translational Science Center, University of New Mexico, Albuquerque, New Mexico, United States of America
- Center for Global Health, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Darrell L. Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
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Cruz GLT, Winck GR, D'Andrea PS, Krempser E, Vidal MM, Andreazzi CS. Integrating databases for spatial analysis of parasite-host associations and the novel Brazilian dataset. Sci Data 2023; 10:757. [PMID: 37919263 PMCID: PMC10622529 DOI: 10.1038/s41597-023-02636-8] [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: 06/20/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023] Open
Abstract
Incomplete information on parasites, their associated hosts, and their precise geographical location hampers the ability to predict disease emergence in Brazil, a continental-sized country characterised by significant regional disparities. Here, we demonstrate how the NCBI Nucleotide and GBIF databases can be used as complementary databases to study spatially georeferenced parasite-host associations. We also provide a comprehensive dataset of parasites associated with mammal species that occur in Brazil, the Brazilian Mammal Parasite Occurrence Data (BMPO). This dataset integrates wild mammal species' morphological and life-history traits, zoonotic parasite status, and zoonotic microparasite transmission modes. Through meta-networks, comprising interconnected host species linked by shared zoonotic microparasites, we elucidate patterns of zoonotic microparasite dissemination. This approach contributes to wild animal and zoonoses surveillance, identifying and targeting host species accountable for disproportionate levels of parasite sharing within distinct biomes. Moreover, our novel dataset contributes to the refinement of models concerning disease emergence and parasite distribution among host species.
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Affiliation(s)
- Gabriella L T Cruz
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios (LABPMR), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- Programa de Pós-graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- Pró-Reitoria de Pós-Graduação, Pesquisa e Inovação (PROPGPI), Universidade Federal do Estado do Rio de Janeiro (Unirio), Rio de Janeiro, RJ, Brazil
| | - Gisele R Winck
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios (LABPMR), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Paulo S D'Andrea
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios (LABPMR), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Eduardo Krempser
- Plataforma Institucional Biodiversidade e Saúde Silvestre (PIBSS), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Mariana M Vidal
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios (LABPMR), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Cecilia S Andreazzi
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios (LABPMR), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.
- International Platform for Science, Technology and Innovation in Health (PICTIS), Ílhavo, Portugal.
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain.
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