Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories.
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...
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ftdoajarticles:oai:doaj.org/article:a4d014131cd7433cb21dc7ef0cb282d5 2024-09-09T19:27:29+00:00 Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. Paris S Salazar-Hamm William L Johnson Robert A Nofchissey Jacqueline R Salazar Publio Gonzalez Samuel M Goodfellow Jonathan L Dunnum Steven B Bradfute Blas Armién Joseph A Cook Daryl B Domman Darrell L Dinwiddie 2024-01-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0011672 https://doaj.org/article/a4d014131cd7433cb21dc7ef0cb282d5 EN eng Public Library of Science (PLoS) https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0011672&type=printable https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0011672 https://doaj.org/article/a4d014131cd7433cb21dc7ef0cb282d5 PLoS Neglected Tropical Diseases, Vol 18, Iss 1, p e0011672 (2024) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2024 ftdoajarticles https://doi.org/10.1371/journal.pntd.0011672 2024-08-05T17:49:24Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 18 1 e0011672 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
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Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Paris S Salazar-Hamm William L Johnson Robert A Nofchissey Jacqueline R Salazar Publio Gonzalez Samuel M Goodfellow Jonathan L Dunnum Steven B Bradfute Blas Armién Joseph A Cook Daryl B Domman Darrell L Dinwiddie Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Paris S Salazar-Hamm William L Johnson Robert A Nofchissey Jacqueline R Salazar Publio Gonzalez Samuel M Goodfellow Jonathan L Dunnum Steven B Bradfute Blas Armién Joseph A Cook Daryl B Domman Darrell L Dinwiddie |
author_facet |
Paris S Salazar-Hamm William L Johnson Robert A Nofchissey Jacqueline R Salazar Publio Gonzalez Samuel M Goodfellow Jonathan L Dunnum Steven B Bradfute Blas Armién Joseph A Cook Daryl B Domman Darrell L Dinwiddie |
author_sort |
Paris S Salazar-Hamm |
title |
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
title_short |
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
title_full |
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
title_fullStr |
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
title_full_unstemmed |
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
title_sort |
choclo virus (chov) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2024 |
url |
https://doi.org/10.1371/journal.pntd.0011672 https://doaj.org/article/a4d014131cd7433cb21dc7ef0cb282d5 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 18, Iss 1, p e0011672 (2024) |
op_relation |
https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0011672&type=printable https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0011672 https://doaj.org/article/a4d014131cd7433cb21dc7ef0cb282d5 |
op_doi |
https://doi.org/10.1371/journal.pntd.0011672 |
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PLOS Neglected Tropical Diseases |
container_volume |
18 |
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1 |
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e0011672 |
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