Molecular characterization of rodent- and-shrew-borne viruses and the prevalence and intensity of infestation of small mammal fleas, in Namibia

A thesis submitted in fulfillment of the requirements for the Degree of Master of Science

Small mammals host diverse communities of both ectoparasites (e.g. fleas and ticks) and endoparasites (e.g. bacteria and viruses). Some parasites are vectors of diseases that infect both humans and wildlife. The main objective of the study was to discover and molecularly characterize novel Hantaviruses and Arenaviruses and to determine the prevalence and intensity of fleas on small mammals in selected areas of Namibia. Small mammals were trapped from six different regions and screened for both Hantavirus and Arenavirus. The regions are, namely, Hardap, Khomas, Kunene, Okavango, Omaheke, and Otjozondjupa. Nucleotide sequence analysis of PCR of the partial large segments of both a Hantavirus and Arenavirus were amplified from RNA extracted from the lungs of small mammal hosts. Hantaviruses were not prevalent in any of the small mammals trapped. However, two new Arenaviruses, not previously recorded in Namibia were both isolated from the Namaqua rock mouse, Micaelamys namaquensis, trapped in Okahandja and Mariental. The Arenavirus isolated from rodents trapped in Okahandja and Mariental respectively, is closely related to the Merino Walk virus isolated from the Bush vlei rat, Myotomys unisulcatus, captured in South Africa and Luna virus discovered in Zambia in the host, the Natal multimammate mouse, Mastomys natalensis. A generalised linear model (GLM) was used to analyse the significant influence that different factors would present on the prevalence and intensity of flea infestation in three (Hardap, Khomas and Okavango, of the six regions. Factors tested for included host sex, body mass, head-body length and reproductive status. A total of 358, fleas belonging to 9 species (Chiastopsylla rossi, Xenopsylla cheopis, X. brasiliensis, X. hirsuta, X. nubica, X. philoxera, X. piriei, X. versuta, Listropsylla aricinae) were recovered. These fleas were recovered from 5 rodent species, namely Gerbilliscus leucogaster, Mastomys sp., M. namaquensis, Rhabdomys pumilio and Saccostomus campestris. Fleas were prevalent in only 52.3% of the hosts (114 small mammals) examined, of which 54.4% were female and 89.5% were breeding. The GLM analysis showed that host sex, body mass and head body length (representing size of the hosts) and reproductive status of hosts, did not significantly influence the prevalence of fleas on hosts in the three regions (p = 0.225, 0.053, 0.275, 0.086, respectively). Male hosts had a significantly high intensity of infestation of fleas compared to females, in Mariental (p = 0.005). Host body mass had a significant effect on the intensity of infestation of fleas in Neudamm (p = 0.003), whereas host head-body length exerted significantly influence on the intensity of infestation (p = 0.005). Gerbilliscus leucogaster was the only host species represented, in comparable numbers, in all three regions of study. The results of GLM analysis revealed that there was no significant difference in both the prevalence and intensity of infestation of G. leucogaster in the three regions of study. The use of PCR has revealed the presence of rodent-borne Arenaviruses. Various factors that possibly influence the intensity and prevalence of flea infestation in small mammals have been determined using the GLM analysis.