Coinfections in East African Shorthorn Zebu

Abstract

The Infectious Diseases of East African Livestock (IDEAL) project followed 548 East African Shorthorn Zebu (EASZ) calves in Western Kenya for the first year of life and monitored the sequelae of infections by multiple parasites. More than 50 different parasites were identified during this time. The IDEAL project also gathered environmental information about the farm and collected phenotypic data on the calf and its dam. Calves were also genotyped for 55,777 single nucleotide polymorphisms (SNPs). Recent research has looked at coinfection in rodents and humans but not in indigenous cattle. Here I investigate the evidence for coinfection in EASZ and study the associations occurring between coinfecting parasites. In addition, I examine the genetic and phenotypic factors which predispose an individual to infection with multiple parasites. Using information gathered by the IDEAL project, my thesis consists of the following chapters. An investigation of the nature of concurrent associations and of lagged effects between different parasites. Using the parasites Theileria spp., Coccidia spp., Strongyloides spp., strongyles and Calicophoron spp. I show that the patterns of association between different parasites are complex: there is evidence for both positive and negative associations. For example, infection with Strongyloides spp. increased the risk of strongyle infection. Conversely, in other cases, being infected with one parasite decreased the calf’s risk of infection with another parasite: for example, infection with Strongyloides spp. decreased the risk of infection with Calicophoron spp. A study of the relationship between different respiratory viruses and their effect upon the host. I confirm that positive associations exist between Infectious Bovine Rhinotracheitis (IBR), Bovine Viral Diarrhoea Virus (BVDV) and Bovine Parainfluenza Virus Type 3 (PIV3) in a previously unstudied setting; being seropositive for any one of these three viruses means that an individual is more likely to be seropositive for the other two viruses than expected by chance. Being seropositive for IBR, BVDV or PIV3 did not affect the average daily weight gain of the calf, nor did PIV3 and BVDV serostatus have an effect on the calf ever experiencing a clinical episode. However, IBR seropositive calves were less likely to experience a clinical episode of some form, suggestive of some protective aspect of IBR. An examination of the sources of variation in faecal strongyle egg counts (EPG), and their association with body weight, host genetics and a suite of haematological measures. Using estimates of relatedness derived from the SNP data, I established that strongyle EPG has a genetic basis in EASZ, with a heritability of 23.9% (S.E. = 11.8%) and showed a consistently strong negative association between strongyle infection and the haematological parameters white blood cell count, red blood cell count, total serum protein and absolute eosinophil count. Furthermore, calf body weight at 1 week old was a significant predictor of strongyle EPG at 16-51 weeks, with smaller calves being predisposed to a higher strongyle EPG later in life. A genome-wide association study (GWAS) to investigate if there is a genetic predisposition to East Coast Fever (ECF) death and a genetic basis to the packed cell volume at the time of seroconversion to Theileria parva (PCVTP). I found no robust evidence for a relationship between genotyped single nucleotide polymorphisms (SNPs) and ECF death or PCVTP. The effect of sample size upon GWAS and significance thresholds was investigated further through simulations. I conclude that the small number of cases influences the probability of association between a SNP and the phenotypic trait. Smaller case numbers produce more artifactual associations with SNPs, an effect not fully compensated for by the standard Bonferroni correction, suggesting that an empirical significance threshold should be used to directly account for sample size. The results of this thesis provide an understanding of the associations occurring between different parasites, and of their causes and consequences. I discuss the results in the context of their implications for disease control strategies, suggesting the benefits of an integrated approach to control worm and T. parva alongside the possible genetic selection for parasite resistance and supplementary feeding of lightweight individuals to improve the health of EASZ.