Many emerging infections are RNA virus spillovers from animal reservoirs. Reservoir identification is necessary for predicting the geographic extent of infection risk, but rarely are taxonomic levels below the animal species considered as reservoir, and only key circumstances in nature and methodology allow intrinsic virus-host associations to be distinguished from simple geographic (co-)isolation. We sampled and genetically characterized in detail a contact zone of two subtaxa of the rodent Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo and Morogoro virus, each spatially confined to a single M. natalensis subtaxon, only co-occurring at the contact zone’s centre. Inter-subtaxon hybridization at this centre and a continuum of quality habitat for M. natalensis show that both viruses have the ecological opportunity to spread into the other substaxon’s range, but do not, strongly suggesting host-intrinsic barriers. Such barriers could explain why human cases of another M. natalensis-borne arenavirus, Lassa virus, are limited to West Africa. Reservoirs of zoonotic viruses are usually equated with a particular wildlife species. It is rarely assessed whether genetic groups below the species level may instead represent the actual reservoir, though this would have major implications on estimations of the zoonosis’ spatial distribution. Here we investigate whether geographically and genetically distinct subtaxa of the widespread African rodent Mastomys natalensis carry distinct arenaviruses, by sampling in detail across a contact zone of two of these subtaxa. Ongoing hybridization shows that individuals of the subtaxa are in direct physical contact, in principle allowing viral exchange, yet neither of the two arenaviruses -Gairo and Morogoro virus- were found to have crossed the zone. Such intraspecific genetic barriers to arenavirus spatial spread have important implications for our understanding of the related Lassa arenavirus, a pathogen potentially lethal to humans of which Mastomys natalensis is also the main reservoir. Although Lassa virus appears to infect several secondary hosts, its distribution is restricted to West Africa and matches that of another M. natalensis subtaxon. Our data thus indicates that it is because of M. natalensis intraspecific distinctions that the human Lassa fever endemic area has not expanded to the rest of sub-Saharan Africa.

Rodent management in agriculture remains a major challenge in developing countries where resource-poor farmers are ill equipped to deal with pest species. It is compounded by unpredictable outbreaks, late control actions, lack of/or inadequate expert interventions, expensive rodenticides and other factors. Ecologically based rodent management (EBRM) is recommended as the way forward for rodent management in Africa. EBRM relies on understanding the ecology of pest species and formulating this knowledge into management programs. The present paper evaluates the potential for establishing EBRM in Africa and the challenges that have to be overcome to implement it. The major constraints for establishing EBRM in Africa include the absence of key studies on the taxonomy and ecology of rodents, inadequate research on EBRM, lack of knowledge by farmers on available technologies and agricultural policies that are unfavourable. The development of EBRM and its success in Asia is a strong encouragement to African scientists to develop similar management strategies for the most important pest species such as the multimammate rats, Mastomys natalensis. EBRM initiatives such as the Development of Ecologically Based Rodent Management for the Southern Africa Region (ECORAT) project undertook studies on e.g. rodent ecology, taxonomy, knowledge, attitude and practices and rodent–human interactions in rural agricultural communities. Through this project, EBRM interventions were introduced in Tanzania, Swaziland and Namibia to provide solutions to local rodent-pest problems. Intervention actions including community-based intensive trapping of rodents, habitat manipulation and sanitary measures demonstrated that the impacts of rodents on communities could be drastically reduced. EBRM programs in Africa must address how to change attitudes of target communities, building scientific capacity, implanting rodent-management skills by translating the developed technologies and strategies into simple understandable and easy-to-implement actions and influencing policy makers to accept the concepts and practices to be introduced. Further, we need to demonstrate that EBRM is economically feasible and sustainable and that through community participation, EBRM will become deeply rooted in those communities.

This study investigated mammalian involvement in an outbreak of bubonic plague in Mbulu District, northern Tanzania, in March 2007. Plague is a rodent-borne zoo- notic disease that spreads to humans through fleas infected with Yersinia pestis. Live trapping of rodents and shrews was conducted in fallow and crop fields, peri- domestic areas, houses and the neighboring forest reserve. Serum was separated from blood of captured animals. A rapid diagnostic test (RDT) was used for diag- nosis of plague infection. An ELISA technique was used to detect antibodies against Yersinia pestis fraction 1 antigen. Wild and commensal rodents tested positive by RDT, indicating current infection in clinically healthy ani- mals. The ELISA showed that wild rodents (Lophuromys flavopunctatus, Praomys delectorum, Graphiurus muri- nus, Lemniscomys striatus) and commensal rats (Rattus rattus, Mastomys natalensis, Mus minutoides) were Y. pestis-positive. Two potential vectors, Xenopsylla brasi- liensis and Dinopsyllus lypusus, were found on wild and commensal rodents with a flea index of 1.8. We conclude that diverse potential mammalian reservoirs and efficient vectors of Y. pestis are present in abundance in Dongo- besh and could lead to persistence and future plague outbreaks.