A 19 Year Analysis of Small Mammals Associated with Human Hantavirus Cases in Chile

Viral shedding and viraemia of Andes virus during acute hantavirus infection: a prospective study

BACKGROUND

Andes virus (ANDV) is a zoonotic Orthohantavirus leading to hantavirus cardiopulmonary syndrome. Although most transmissions occur through environmental exposure to rodent faeces and urine, rare person-to-person transmission has been documented, mainly for close contacts. This study investigates the presence and infectivity of ANDV in body fluids from confirmed cases and the duration of viraemia.

METHODS

In this prospective study, 131 participants with confirmed ANDV infection were enrolled in Chile in a prospective study between 2008 and 2022. Clinical samples (buffy coat, plasma, gingival crevicular fluid [GCF], saliva, nasopharyngeal swabs [NPS], and urine) were collected weekly for 3 weeks together with clinical and epidemiological data. Samples were categorised as acute or convalescent (up to and after 16 days following onset of symptoms). Infectivity of positive fluids was assessed after the culture of samples on Vero E6 cells and use of flow cytometry assays to determine the production of ANDV nucleoprotein.

FINDINGS

ANDV RNA was detected in 100% of buffy coats during acute phase, declining to 95% by day 17, and to 93% between days 23-29. ANDV RNA in GCF and saliva decreased from 30% and 12%, respectively, during the acute phase, to 12% and 11% during the convalescent phase. Successful infectivity assays of RT-qPCR-positive fluids, including GCF, saliva, NPS, and urine, were observed in 18 (42%) of 43 samples obtained during the acute phase of infection. After re-culture, the capacity to infect Vero E6 cells was maintained in 16 (89%) of 18 samples. Severity was associated with the presence of ANDV RNA in one or more fluids besides blood (odds ratio 2·58 [95% CI 1·42-5·18]).

INTERPRETATION

ANDV infection is a systemic and viraemic infection, that affects various organs. The presence of infectious particles in body fluids contributes to our understanding of potential mechanisms for person-to-person transmission, supporting the development of preventive strategies. Detection of ANDV RNA in additional fluids at hospital admission is a predictor of disease severity.

FUNDING

None.

TRANSLATION

For the Spanish translation of the abstract see Supplementary Materials section.

Mathematical Model of the Spread of Hantavirus Infection

A mathematical epidemiological model incorporating the mobility of rodents and human groups among zones of less or major contact between them is presented. The hantavirus infection dynamics is expressed using a model type SEIR (Susceptible-Exposed-Infectious-Removed), which incorporates the displacement of the rodent and the human, between the urban and rural sector, the latter being subdivided in populated and non-populated. The results show the impact that rodent or human displacement may have on the propagation of hantavirus infection. Human mobility is more significant than rodents in increasing the number of hantavirus infection cases. The results found may be used as a reference by the health authorities to develop more specific campaigns on the territorial dynamics of the rodent, attend to the mobility of humans in these territories, mainly agricultural and forestry workers, and strengthen control-prevention actions in the community, to prevent future outbreaks that are fatal.

Deep Sequencing to Reveal Phylo-Geographic Relationships of Juquitiba Virus in Paraguay

Several hantaviruses result in zoonotic infections of significant public health concern, causing hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in the Old and New World, respectively. Given a 35% case fatality rate, disease-causing New World hantaviruses require a greater understanding of their biology, genetic diversity, and geographical distribution. Juquitiba hantaviruses have been identified in Oligoryzomys nigripes in Brazil, Paraguay, and Uruguay. Brazil has reported the most HCPS cases associated with this virus. We used a multiplexed, amplicon-based PCR strategy to screen and deep-sequence the virus harbored within lung tissues collected from Oligoryzomys species during rodent field collections in southern (Itapúa) and western (Boquerón) Paraguay. No Juquitiba-like hantaviruses were identified in Boquerón. Herein, we report the full-length S and M segments of the Juquitiba hantaviruses identified in Paraguay from O. nigripes. We also report the phylogenetic relationships of the Juquitiba hantaviruses in rodents collected from Itapúa with those previously collected in Canindeyú. We showed, using the TN93 nucleotide substitution model, the coalescent (constant-size) population tree model, and Bayesian inference implemented in the Bayesian evolutionary analysis by sampling trees (BEAST) framework, that the Juquitiba virus lineage in Itapúa is distinct from that in Canindeyú. Our spatiotemporal analysis showed significantly different time to the most recent ancestor (TMRA) estimates between the M and S segments, but a common geographic origin. Our estimates suggest the additional geographic diversity of the Juquitiba virus within the Interior Atlantic Forest and highlight the need for more extensive sampling across this biome.

Activity patterns and interactions of rodents in an assemblage composed by native species and the introduced black rat: implications for pathogen transmission

Background

The degree of temporal overlap between sympatric wild hosts species and their behavioral interactions can be highly relevant to the transmission of pathogens. However, this topic has been scantly addressed. Furthermore, temporal overlap and interactions within an assemblage of wild rodents composed of native and introduced species have been rarely discussed worldwide. We assessed the nocturnal activity patterns and interactions between rodent taxa of an assemblage consisting of native species (Oligoryzomys longicaudatus, Abrothrix hirta, and Abrothrix olivaceus) and the introduced black rat (Rattus rattus) in a temperate forest from southern Chile. All rodent species in this study are known hosts for various zoonotic pathogens.

Results

We found a high nocturnal temporal overlap within the rodent assemblage. However, pairwise comparisons of temporal activity patterns indicated significant differences among all taxa. Rattus rattus showed aggressive behaviors against all native rodents more frequently than against their conspecifics. As for native rodents, agonistic behaviors were the most common interactions between individuals of the same taxon and between individuals of different taxa (O. longicaudatus vs Abrothrix spp.).

Conclusions

Our findings reveal several interactions among rodent taxa that may have implications for pathogens such as hantaviruses, Leptospira spp., and vector-borne pathogens. Furthermore, their transmission may be facilitated by the temporal overlap observed between rodent taxa.

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countries) and new communication pipelines that connect biorepositories and biomedical communities. To this end, we highlight a novel adaptation of Project ECHO’s virtual community of practice model: Museums and Emerging Pathogens in the Americas (MEPA). MEPA is a virtual network aimed at fostering communication, coordination, and collaborative problem-solving among pathogen researchers, public health officials, and biorepositories in the Americas. MEPA now acts as a model of effective international, interdisciplinary collaboration that can and should be replicated in other biodiversity hotspots. We encourage deposition of wildlife specimens and associated data with public biorepositories, regardless of original collection purpose, and urge biorepositories to embrace new specimen sources, types, and uses to maximize strategic growth and utility for EID research. Taxonomically, geographically, and temporally deep biorepository archives serve as the foundation of a proactive and increasingly predictive approach to zoonotic spillover, risk assessment, and threat mitigation.

Behavioral Responses of Wild Rodents to Owl Calls in an Austral Temperate Forest

Simple Summary

Growing human populations are challenging scientists to find effective ways to control and mitigate human–wildlife conflict while preserving biodiversity. It has been reported that predator odor and calls can drive away rodents, but little is known about species-specific responses of prey. For these reasons, we compared the behavioral changes of common rodent species inhabiting the Chilean temperate forest (Abrothrix spp., the long-tailed pygmy rice rat Oligoryzomyslongicaudatus and the black rat Rattus rattus) when exposed to two different native predator calls (the austral pygmy owl Glaucidium nana and the rufous-legged owl Strix rufipes) and a control (no predator calls). Our results showed that all rodent species modified their behavior in the presence of predator calls, but the effects were species dependent. These findings point to the need to carefully study target rodent species instead of applying a general control plan for all rodent species.

Abstract

Ecologically based rodent management strategies are arising as a sustainable approach to rodent control, allowing us to preserve biodiversity while safeguarding human economic activities. Despite predator signals being known to generally repel rodents, few field-based studies have compared the behavioral effects of several predators on different prey species, especially in Neotropical ecosystems. Here, we used camera traps to study the behavior of rodent species native to the Chilean temperate forest (Abrothrix spp., long-tailed pygmy rice rat Oligoryzomys longicaudatus) and an introduced rodent (black rat Rattus rattus). Using playbacks of raptor calls, we experimentally exposed rodents to three predation risk treatments: austral pygmy owl calls (Glaucidium nana), rufous-legged owl calls (Strix rufipes) and a control treatment (absence of owl calls). We evaluated the effects of the treatments on the time allocated to three behaviors: feeding time, locomotor activity and vigilance. Moonlight and vegetation cover were also considered in the analyses, as they can modify perceived predation risk. Results showed that predator calls and environmental factors modified prey behavior depending not only on the predator species, but also on the rodent species. Consequently, owl playbacks could be regarded as a promising rodent control tool, knowing that future studies would be critical to deeply understand differences between species in order to select the most effective predator cues.