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

Document Type

Article

Publication Date

1-1-2024

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.

Publication Title

PLoS Negl Trop Dis

ISSN

1935-2735

Volume

18

Issue

1

First Page

0011672

Last Page

0011672

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