Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis

Abstract

The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically sampled and archived rodents from >150 sites across Panama to establish a baseline understanding of the host and virus, producing a permanent archive of holistic specimens that we are now probing in greater detail. We summarize these collections and explore preliminary habitat/virus associations to guide future wildlife surveillance and public health efforts related to CHOV and other zoonotic pathogens. Host sequences of the mitochondrial cytochrome b gene form a single monophyletic clade in Panama, despite wide distribution across Panama. Seropositive samples were concentrated in the central region of western Panama, consistent with the ecology of this agricultural commensal and the higher incidence of CHOV in humans in that region. Hantavirus seroprevalence in the pygmy rice rat was >15% overall, with the highest prevalence in agricultural areas (21%) and the lowest prevalence in shrublands (11%). Host–pathogen distribution, transmission dynamics, genomic evolution, and habitat affinities can be derived from the preserved samples, which include frozen tissues, and now provide a foundation for expanded investigations of orthohantaviruses in Panama.

Choclo virus (CHOV) recovered from deep metatranscriptomics of archived museum tissues

“…This is reflective of the clinical disease burden with the greatest number of cases in Los Santos (77%) followed by Veraguas (12%) and Coclé (7%) [12]. The strains from the province of Panamá form a well-supported clade demonstrating potential geographic substructure (Fig 4) which is congruent with previous findings [39]. More sequencing is needed to determine how closely these are related to clinical strains; however, only seven Panamá residents have reported HCPS in the last 20 years (1% of all cases) [12].…”

“…An outbreak from late 1999 to early 2000 of hantavirus cardiopulmonary syndrome (HCPS) in western Panama [9,10] has spurred over two decades of epidemiological and wildlife surveillance [12,39]. During those 20 years 712 clinical cases of HCPS were reported in Panama [12] and >11,000 specimens of non-volant mammals with archived biological materials were contributed to museum repositories (https://arctos.database.museum/).…”

“…During those 20 years 712 clinical cases of HCPS were reported in Panama [12] and >11,000 specimens of non-volant mammals with archived biological materials were contributed to museum repositories (https://arctos.database.museum/). Of these, just shy of 800 rodents have been currently screened for prior hantavirus infection using an IgG strip immunoblot assay [40] with an average seropositivity of 16% [39]. We requested samples designated hantavirus positive at the University of New Mexico Southwestern Museum of Biology for metatranscriptomic sequencing.…”

“…Although we only present samples here with sequence data, previous surveillance efforts have found hantavirus seropositive O. costaricensis across its broad geographic range in Panama in five out of the nine ecoregions: Central American Atlantic Moist Forests, Isthmian-Pacific Moist Forests, Panamanian Dry Forests, Pacific Mangrove S. America, and Choco/Darién Moist Forests [39].…”

Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories

“…The administrative political division of the Panamanian map was generated by the Topography Department of the National Institute of Statistics and Census of the General Comptroller of the Republic of Panama ( https://www.inec.gob.pa/ ). A spatial representation of the human cases and rodent capture sites were georeferenced using the Datum UTM, WGS 1984, with ArcMap software from ArcGIS v.10.7 (ESRI2019) [ 36 ]. Samples collected within 12 km were aggregated based on maximum spatial movements of close rodent relatives [ 37 , 38 ].…”