Genetic Diversity of Hepatitis B and Hepatitis C Viruses in Ethiopia

Hepatitis B and C viruses are a major cause of mortality and morbidity worldwide. In 2015 alone, viral hepatitis caused 1.34 million deaths, a number comparable to annual deaths caused by tuberculosis but higher than those caused by either HIV or malaria. However, in contrast to these three infectious diseases, viral hepatitis has received relatively little attention. Worldwide, only 9% of HBV-infected and 20% of HCV-infected persons have access to affordable hepatitis testing. Even more worrisome is the fact that only 8% of those diagnosed with HBV and 7.4% of those diagnosed with HCV had started treatment. This is even more problematic in low-income countries like Ethiopia where more than 80% of the population are living in rural areas with a very limited access to healthcare and where viral hepatitis has never been considered a major health priority. Most importantly, the clinical and treatment outcomes of HBV and HCV infections are largely influenced by the high genetic diversity (genotype, subgenotype, recombinants and quasispecies variants) of these viruses that also display distinct geographical distribution worldwide. In this thesis, therefore, we studied the seroepidemiology of HBV and HCV infection and determined the molecular epidemiology and genetic diversity of HBV and HCV in different geographic regions of Ethiopia. We identified that genotype A (A1) and genotype D (D2 and novel D10) of HBV and genotype 4 ( 4d and 4r ) of HCV are the most prevalent in Ethiopia. We further analyzed HBV and HCV quasispecies variants and their association with patients’ clinical characteristics using ultra-deep sequencing approach and found some important variants

Evaluation of direct colorimetric MTT assay for rapid detection of rifampicin and isoniazid resistance in Mycobacterium tuberculosis

With the spread of multidrug-resistant tuberculosis (MDR-TB) strains there is an increasing need for new accurate and cost-effective methods for a rapid diagnostic and drug susceptibility testing (DST), particularly in low-income countries where tuberculosis is hyperendemic. A colorimetric assay using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) has been suggested as a promising method for DST, especially to rifampicin. In this study, we standardized and evaluated the MTT assay for a rapid direct detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis strains from sputum specimens using Lowenstein-Jensen (LJ) culture medium as a gold standard. The MTT assay sensitivity, specificity, positive and negative predictive values for rifampicin were 100%, 86%, 100%, 99%, respectively. For isoniazid, the MTT assay had a 100% sensitivity, specificity, positive and negative predictive values. Interestingly, the MTT assay gave interpretable results within two weeks for 94% of the samples compared to 7-14 weeks for LJ media. Overall, an excellent agreement was observed between MTT assay and LJ proportion method (Kappa, 0.91 for rifampicin and 1.00 for isoniazid). In conclusion, the direct colorimetric MTT assay simultaneously detects susceptible and resistant strains of M. tuberculosis within three weeks. It significantly shortens the time required to obtain a DST result and could be a reliable alternative method for rapid detection of drug-resistant TB strains in high-TB-burden resource-limited settings

Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts

Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progression has not been fully defined and tools aiding the deconvolution of complex patient virus profiles is an unmet clinical need. Vari