about

ABOUT


# _Calomys callosus_

## Common Name
Large Vesper Mouse

## Host for Diseases:
[Bolivian Hemorrhagic Fever (Machupo Virus), Chagas](https://www.sciencedirect.com/science/article/pii/S1879625714000558?ref=pdf_download&fr=RR-2&rr=929db80edbef34030)

## Family Structure
Litter sizes range between 3-5 pups and the adults who weigh between 30-50 grams, do not show sexual dimorphism.

## Habitat
It is a nocturnal mice species that is generalist in its habitat and has a wide distribution. Found primarily in Bolivia, it has also been reported in Argentina, Paraguay, and Brazil. Due to their generalist habitation patterns, they can inhabit a variety of ecological niches including agricultural fields and homes.

## Epidemiology
The rodent spreads the Machupo virus primarily to agricultural workers, but it can also cause infections in urban areas. Infections peak from [June to August](https://www.sciencedirect.com/science/article/pii/B9780702051012000170) with the drier climate. Historical outbreaks have been tied to [pesticide use](https://www.sciencedirect.com/science/article/pii/S1879625714000558?ref=pdf_download&fr=RR-2&rr=929db80edbef3403).


Calomys callosus


# _Calomys laucha_

## Common Name
Small Vesper mouse

## Host for Diseases:
Argentine Hemorrhagic fever (Junin Virus), [Hantavirus Pulmonary Syndrome (Laguna Negra Virus)](https://pubmed.ncbi.nlm.nih.gov/11791973/)

## Family Structure
Adults weigh approximately 13 grams. Litter size can range from 5 to 10 pups per litter and they follow a monogamous mating and nesting system.

## Habitat
Primarily found in the Chaco plains of Argentina, Bolivia, Paraguay, south eastern Brazil, small parts of Uruguay and Chile. The mice prefer dryer, flat plains with crops or grass covered areas and where soil is sandy that helps them create burrows. Key ecological characteristics include seasonal changes to habitat selection where high vegetation areas are preferred in summer and winters are marked by more peri-domestic and open habitats.

## Epidemiology
This rodent spreads the Junin virus primarily to [agricultural workers](https://www.sciencedirect.com/science/article/pii/B9780702051012000170), who are exposed to aerosols by the rodents living within their fields. Cases peak from March to June and [every 3-5 years](https://www.sciencedirect.com/science/article/pii/B9780123751560000308?ref=pdf_download&fr=RR-2&rr=929db02cadd83403), with increased argicultural activity during harvests and peaks in the rodent population.


Calomys laucha


# _Calomys musculinus_

## Common Name

[Drylands Vesper mouse](https://www.gbif.org/species/2437951)

## Host for Diseases:

Argentine Hemorrhagic Fever (Junin Virus), Chagas

## Family Structure:

The rodent is polygamous and has litters of 6.1-7.5 offspring.

## Habitat

The rodent lives in Argentina, Paraguay, and Bolivia. [It can be found in argicultural fields](https://www.sciencedirect.com/science/article/pii/B9780702051012000170).

## Epidemiology

This rodent spreads the Junin virus primarily to agricultural workers, who are exposed to aerosols by the rodents living within their fields. Cases peak from March to June and [every 3-5 years](https://www.sciencedirect.com/science/article/pii/B9780123751560000308?ref=pdf_download&fr=RR-2&rr=929db02cadd83403), with increased argicultural activity during harvests and peaks in the rodent population.


Calomys musculinus

# Guanarito virus

## Causal Agent of:
Venezuelan Hemorrhagic Fever (VHF)

## History
Found first in rural Venezuela, Guanarito virus was named after the city of Guanarito where it was found in Portuguese province of Venezuela in 1988-1990. VHF is can be severe in some cases with an estimate of 25% mortality just like Argentine Hemorrhagic fever (AHF) and Lassa Fever (LF) which are also caused by arenaviruses. The most risk-prone groups include migrant agricultural workers (mostly male) and their families. The [last reported outbreak](<https://doi.org/10.1016/0140-6736(91)91899-6>) was seen in early 1990s.

## Reservoirs
[Short-tailed cane mouse](resources?item=zygodontomys_brevicauda) (_Zygodontomys brevicauda_) (confirmed) and [Alston's Cotton rat](resources?item=sigmodon_alstoni) (_Sigmodon alstoni_) (suspected)


## Species distribution models for reservoirs of Guanarito virus

We conducted a study to (i) model the species distribution of the two rodent species, namely, _Z. brevicauda_ and _S. alstoni_ using climate-driven features such as [bioclimatic features](https://www.worldclim.org/data/bioclim.html), [land use](https://lcluc.umd.edu/), [NDVI](https://modis.gsfc.nasa.gov/data/dataprod/mod13.php), and [elevation/ topography](https://portal.opentopography.org/datasetMetadata?otCollectionID=OT.032021.4326.2) and (ii) attempt to predict how the species distribution will change in response to changes in the climate-driven features in the future based on climate change scenarios derived from [CMIP6](https://www.carbonbrief.org/cmip6-the-next-generation-of-climate-models-explained/#:~:text=model%20sensitivity%20values.-,Future%20warming%20in%20CMIP6,-The%20limited%20number). More specifically, [the moderate climate change scenario or SSP2.45 and severe climate change scenario or SSP5.85](https://www.carbonbrief.org/explainer-the-high-emissions-rcp8-5-global-warming-scenario/#:~:text=The%20new%20SSP%20scenarios).

Each species was found to be sensitive to different features and the changes therein. Following figure shows the feature importances based on the mean reduction in impurity of the classification algorithms (a) with Recursive Feature Selection([RFE](https://scikit-learn.org/dev/modules/generated/sklearn.feature_selection.RFE.html)) and (b) without [RFE](https://scikit-learn.org/dev/modules/generated/sklearn.feature_selection.RFE.html).

 

![Fig a. Feature importances for four classification algorithms respectively with RFE](/markdown/images/RFE_guan.png)

 

![Fig b. Feature importances for four classification algorithms respectively without RFE](/markdown/images/noRFE_guan.png)

Guanarito virus


AtlasArena is a **Wellcome Trust**-funded research project that aims to create and deploy climate-driven spatio-temporal disease ecology models that predict the risk of infections to humans from new world Arenaviruses. The platform uses Species Distribution Models (SDMs) to predict the geographical distribution of rodent reservoirs for zoonotic New World Arenaviruses, leveraging occurrence data, bioclimatic, vegetation, and land use datasets.


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Climate change alters human risk for infectious diseases

AtlasArena

# Junin Virus

## Causal Agent of:
Argentine Hemorrhagic Fever (AHF)

## History
Junin mammarenavirus (JUNV) or commonly known as Junin virus, is an RNA virus endemic to the humid pampas in Argentina, a densely populated area at the core of the largest agro-industrial complex in the country. In severe cases of AHF, patients develop hemorrhagic and neurological complications, with a fatality rate of 20%. In the last 10 years, [the virus spread has expanded to northeastern Argentina](https://www.biorxiv.org/content/10.1101/2024.06.24.600371v1), with recent reemergence in areas that had not had cases for 15-20 years. 

## Reservoir
_Calomys musculinus_ ([Dryland Vesper Mouse](resources?item=calomys_musculinus)), _Calomys laucha_ ([Small Vesper mouse](resources?item=calomys_laucha)) and _Oligoryzomys flavescens_ ([Yellow Pygmy Rice Rat](resources?item=oligoryzomys_flavescens))

## Species distribution models for reservoirs of Guanarito virus

We conducted a study to (i) model the species distribution of the three rodent species, namely, _C. musculinus_, _C.laucha_ and _O.flavescens_ using climate-driven features such as [bioclimatic features](https://www.worldclim.org/data/bioclim.html), [land use](https://lcluc.umd.edu/), and (ii) attempt to predict how the species distribution will change in response to changes in the climate-driven features in the future based on climate change scenarios derived from [CMIP6](https://www.carbonbrief.org/cmip6-the-next-generation-of-climate-models-explained/#:~:text=model%20sensitivity%20values.-,Future%20warming%20in%20CMIP6,-The%20limited%20number). More specifically, [the moderate climate change scenario or SSP2.45 and severe climate change scenario or SSP5.85](https://www.carbonbrief.org/explainer-the-high-emissions-rcp8-5-global-warming-scenario/#:~:text=The%20new%20SSP%20scenarios).

Each species was found to be sensitive to different features and the changes therein. Following figure shows the feature importances based on the mean reduction in impurity of the classification algorithms (a) with Recursive Feature Selection([RFE](https://scikit-learn.org/dev/modules/generated/sklearn.feature_selection.RFE.html)) and (b) without [RFE](https://scikit-learn.org/dev/modules/generated/sklearn.feature_selection.RFE.html).

 

![Fig a. Feature importances for four classification algorithms respectively with RFE](/markdown/images/RFE_junin.png)

 

![Fig b. Feature importances for four classification algorithms respectively without RFE](/markdown/images/noRFE_junin.png)

Junin virus

# Machupo virus

## Causal Agent of:
Bolivian Hemorrhagic fever (BHF)

## History
Endemic to Bolivia, Machupo virus, like its close relatives [Junin virus](resources?item=junin_virus), [Guanarito virus](resources?item=guanarito_virus) and Chapare virus, is one of the main New World Arenaviruses that cause hemorrhagic fever. The disease is severe and can lead to a case-mortality rate of 25-35% with acute symptoms but may also lead to debilitating chronic viraemia. The [first reported outbreak was in early 1960s and the latest was reported in early 1990s](https://doi.org/10.1016/j.vetmic.2009.08.027). Recently, sporadic and isolated cases have been reported across Bolivia due to changes in human-rodent interactions.

## Reservoir
_Calomys callosus_ ([large vesper mouse](resources?item=calomys_callosus))

## Species Distribution Models for Reservoirs of Machupo virus
We conducted a study to (i) model the species distribution of the rodent species, _Calomys callosus_ using climate-driven features such as [bioclimatic features](https://www.worldclim.org/data/bioclim.html), [land use](https://lcluc.umd.edu/), [NDVI](https://modis.gsfc.nasa.gov/data/dataprod/mod13.php), and [elevation/ topography](https://portal.opentopography.org/datasetMetadata?otCollectionID=OT.032021.4326.2) and (ii) attempt to predict how the species distribution will change in response to changes in the climate-driven features in the future based on climate change scenarios derived from [CMIP6](https://www.carbonbrief.org/cmip6-the-next-generation-of-climate-models-explained/#:~:text=model%20sensitivity%20values.-,Future%20warming%20in%20CMIP6,-The%20limited%20number). More specifically, [the moderate climate change scenario or SSP2.45 and severe climate change scenario or SSP5.85](https://www.carbonbrief.org/explainer-the-high-emissions-rcp8-5-global-warming-scenario/#:~:text=The%20new%20SSP%20scenarios).

Following figure shows the feature importances based on the mean reduction in impurity of the classification algorithms (a) with Recursive Feature Selection([RFE](https://scikit-learn.org/dev/modules/generated/sklearn.feature_selection.RFE.html)) and (b) without [RFE](https://scikit-learn.org/dev/modules/generated/sklearn.feature_selection.RFE.html).

 

![Fig a. Feature importances for four classification algorithms respectively with RFE](/markdown/images/RFE_machupo.png)

 

![Fig b. Feature importances for four classification algorithms respectively without RFE](/markdown/images/noRFE_machupo.png)

Machupo virus



1) The geographic range of the rodent hosts was determined from presence data, gathered from the Global Biodiversity Information Facility.
   
2) Changes in land-use, human density, vegetation, and other environmental factors over time was determined.
   - Data on these factors was gathered from LCLUC, World Clim, NDVI, MODIS
   - Data on these factors gathered for three scenarios: the current day and two climate-change futures.
   - Changes in the environment would affect the geographic range of the rodents and where humans came into contact with them.
     
3) The environmental, land-use, human density, and rodent-presence data was compared to form a Species Distribution Model.
   
4) Areas where humans were likely to come into contact with rodents were marked as hotspots. Changes in where hotspots occurred could be seen by comparing the present-day to the future climate-change scenarios.


name methodology

METHODOLOGY


# _Oligoryzomys flavescens_

## Common Name
Yellow Pygmy Rice Rat

## Host for Diseases:
Argentine Hemorrhagic Fever (Junin Virus), [Hantavirus Pulmonary Syndrome (Andes Virus)](https://pubmed.ncbi.nlm.nih.gov/32034891/)

## Family Structure
Very little is known about their reproductive behavior and unconfirmed reports include a litter size of 3-7 pups and seasonality in reproductive behavior. Adults can weigh around 40 grams.

## Habitat
Most commonly found in Southern Brazil, Uruguay, Northern Argentina. These rats can inhabit arboreal, terrestrial, or semi-aquatic areas, and are typically spotted in pasture or croplands. These rats are nocturnal in nature and do not move outside of natural home range. 

## Epidemiology
This rodent spreads the Junin virus primarily to [agricultural workers](https://www.sciencedirect.com/science/article/pii/B9780702051012000170), who are exposed to aerosols by the rodents living within their fields. Cases peak from March to June and [every 3-5 years](https://www.sciencedirect.com/science/article/pii/B9780123751560000308?ref=pdf_download&fr=RR-2&rr=929db02cadd83403), with increased argicultural activity during harvests and peaks in the rodent population.


Oligoryzomys flavescens

name publication

resources

RESOURCES


# _Sigmodon alstoni_

## Common Name
Altson's cotton rat

## Host for Diseases:
Venezuelan Hemorrhagic Fever (Guanarito Virus)

## Family Structure
Unconfirmed reports of litter size include 3-7 pups.

## Habitat
Alston’s cotton rat is found naturally in the North-eastern part of the continent of South America (countries of Venezuela, Columbia, Suriname, Guyana, Brazil and French Guiana). Its natural habitat is similar to other Sigmodontid rodents that includes flatlands with shrubs, grass and open crop fields on low elevation lands. Most activity of the rats can be observed during daytime (diurnal). 

## Epidemiology
This rodent spreads the Guanarito Virus primarily to agircultural workers, with cases peaking from November to January.


Sigmodon alstoni


# _Zygodontomys brevicauda_

## Common Name
Short-tailed cane mouse

## Host for Diseases: 
Venezuelan Hemorrhagic fever (Gunarito Virus)

## Family Structure
Adults weigh upto 60-80 grams with no sexual dimorphism and a littersize of 5-11 pups. These mice can survive from 1-5 years although detailed information on this is unavailable.

## Habitat 
This mice species has a natural habitat in North-eastern part of the continent of South America (countries of Venezuela, Columbia, Guyana, Suriname, Northern part of Brazil and French Guiana). It can inhabit a varied set of environments ranging from forested and dense grass areas to open agricultural lands but prefers sites close to water bodies. 

## Epidemiology
This rodent spreads the Guanarito Virus primarily to agircultural workers, with cases peaking from November to January.
