Molecular Detection and Characterization of Newcastle Disease Virus from Chickens in Mid-Rift Valley and Central Part of Ethiopia.

Background: Newcastle disease (ND) is a highly infectious poultry disease that causes major economic losses worldwide. The disease is caused by Newcastle Disease Virus (NDV) and early detection and identification of the viral strain is essential. Having knowledge of the NDV strain genotype that circulates in some regions would help in designing an effective vaccine to control the disease. In this regard, there is little information on NDV strain in chickens in mid Rift Valley and the central part of Ethiopia. Therefore, the purpose of this study was to detect and characterize NDV strain genotype from chickens in mid-Rift Valley and the central part of Ethiopia and test whether this NDV strain genotype matches the vaccine strain currently used in the study area. Methods: A total of 98 samples: 78 (tracheal and cloacal) swabs from chicken pools of five and 20 tissue samples were collected. To detect NDV strain, conserved region of the virus Matrix (M) gene was amplified by qRT-PCR. To characterize NDV strain genotypes, M-gene positive samples were specifically re-amplified by conventional PCR targeting the Fusion (F) gene region and sequenced by Sanger method. Results: 13.26% of tested samples were positive for NDV strain in the study area with statistically significant difference (P<0.05) among the study sites. Further characterization of the F genes from NDV strain isolates by phylogenetic analysis indicated that one field isolate clustered with genotype VII whereas three of the isolates clustered to genotype I, II, and III. The isolate of the current NDV strain vaccine in use in the study area clustered with genotype II. Conclusion: The current study indicates the existence of different NDV strain genotype from that of the vaccine strain currently used. Even though large-scale characterization of several isolates is required at national level, the current study laid baseline information for the existence of variations between field NDV strain genotype and vaccine strain currently used against ND in the country.

Low level of HIV-1C integrase strand transfer inhibitor resistance mutations among recently diagnosed ART-naive Ethiopians.

With the widespread use of Integrase strand transfer inhibitors (INSTIs), surveillance of HIV-1 pretreatment drug resistance is critical in optimizing antiretroviral treatment efficacy. However, despite the introduction of these drugs, data concerning their resistance mutations (RMs) is still limited in Ethiopia. Thus, this study aimed to assess INSTI RMs and polymorphisms at the gene locus coding for Integrase (IN) among viral isolates from ART-naive HIV-1 infected Ethiopian population. This was a cross-sectional study involving isolation of HIV-1 from plasma of 49 newly diagnosed drug-naive HIV-1 infected individuals in Addis-Ababa during the period between June to December 2018. The IN region covering the first 263 codons of blood samples was amplified and sequenced using an in-house assay. INSTIs RMs were examined using calibrated population resistance tool version 8.0 from Stanford HIV drug resistance database while both REGA version 3 online HIV-1 subtyping tool and the jumping profile Hidden Markov Model from GOBICS were used to examine HIV-1 genetic diversity. Among the 49 study participants, 1 (1/49; 2%) harbored a major INSTIs RM (R263K). In addition, blood specimens from 14 (14/49; 28.5%) patients had accessory mutations. Among these, the M50I accessory mutation was observed in a highest frequency (13/49; 28.3%) followed by L74I (1/49; 2%), S119R (1/49; 2%), and S230N (1/49; 2%). Concerning HIV-1 subtype distribution, all the entire study subjects were detected to harbor HIV-1C strain as per the IN gene analysis. This study showed that the level of primary HIV-1 drug resistance to INSTIs is still low in Ethiopia reflecting the cumulative natural occurrence of these mutations in the absence of selective drug pressure and supports the use of INSTIs in the country. However, continues monitoring of drug resistance should be enhanced since the virus potentially develop resistance to this drug classes as time goes by.

Effect of sample management on quantitative HIV-1 viral load measurement at Saint Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.

PURPOSE: This study was meant to determine the effect of time to plasma separation, storage duration, freeze-thawing cycle and dilution proportion on the HIV-1 viral load level. METHODS: Experimental study design was employed by collecting 10mL whole blood samples into two EDTA tubes from 88 eligible HIV infected patients at St Paul's Hospital Millennium Medical College. The viral load test was done using Abbott m2000sp/rt analyzer. Data was entered into Microsoft excel and analyzed by SPSS version 20. Repeated measure analysis of variance was used to compare HIV RNA viral load mean difference between different time to plasma separation, storage, freeze-thawing cycles and dilution levels. Post-hoc analysis was employed to locate the place of significant differences. P value less than 0.05 was used to declare statistical significance while viral RNA level of 0.5 log copies/ml was used to determine clinical significance. RESULTS: There was significant HIV-1 RNA viral load log mean difference between plasma separation time at 6 hours (hrs) and 24hrs (p<0.001). There was also significant HIV-1 RNA viral load log mean difference between plasma tested within 6hrs and those stored at 2-8°C for 15 days (p = 0.006), and between plasma stored at 2-8°C for 6 days versus 15 days (p<0.001). There was significant log mean difference between plasma that was exposed to fourth cycle of freeze-thawing after storage at -20°C when compared with plasma tested within 6hrs (p = 0.013). CONCLUSION: Plasma separated at 24hrs, stored at 2-8°C for 15 days or freeze-thawed for four cycles had significant effect on HIV viral load level. However, the differences were not clinically significant at a cut-off viral load level of 0.5 log copies/ml. Avoiding delays to plasma separation beyond 24 hrs, storing at 2-8°C for 15 days and freeze-thawing for no more than 4 cycles is recommended to improve the result quality.