The HIV-1 late domain-2 S40A polymorphism in antiretroviral (or ART)-exposed individuals influences protease inhibitor susceptibility.

BackgroundThe p6 region of the HIV-1 structural precursor polyprotein, Gag, contains two motifs, P7TAP11 and L35YPLXSL41, designated as late (L) domain-1 and -2, respectively. These motifs bind the ESCRT-I factor Tsg101 and the ESCRT adaptor Alix, respectively, and are critical for efficient budding of virus particles from the plasma membrane. L domain-2 is thought to be functionally redundant to PTAP. To identify possible other functions of L domain-2, we examined this motif in dominant viruses that emerged in a group of 14 women who had detectable levels of HIV-1 in both plasma and genital tract despite a history of current or previous antiretroviral therapy.ResultsRemarkably, variants possessing mutations or rare polymorphisms in the highly conserved L domain-2 were identified in seven of these women. A mutation in a conserved residue (S40A) that does not reduce Gag interaction with Alix and therefore did not reduce budding efficiency was further investigated. This mutation causes a simultaneous change in the Pol reading frame but exhibits little deficiency in Gag processing and virion maturation. Whether introduced into the HIV-1 NL4-3 strain genome or a model protease (PR) precursor, S40A reduced production of mature PR. This same mutation also led to high level detection of two extended forms of PR that were fairly stable compared to the WT in the presence of IDV at various concentrations; one of the extended forms was effective in trans processing even at micromolar IDV.ConclusionsOur results indicate that L domain-2, considered redundant in vitro, can undergo mutations in vivo that significantly alter PR function. These may contribute fitness benefits in both the absence and presence of PR inhibitor

Remote Sensing & GIS for Land Cover/ Land Use Change Detection and Analysis in the Semi-Natural Ecosystems and Agriculture Landscapes of the Central Ethiopian Rift Valley

Technical complexities and the high cost of satellite images have hindered the adoption of remote sensing technology and tools for nature conservation works in Ethiopia as in many developing countries. The terrestrial and aquatic ecosystems in Abijjata Shala Lakes National Park (ASLNP) and the Important Bird Areas (IBAs) around the park are considered to be one of the most important home ranges for birds. However, little is known about the effect of land use/land cover (LULC) dynamics, due to lack of technical know how and logistical problems. However, it has been shown in this study that sophisticated image management works are not always relevant. Instead a simple method of utilizing the thermal band has been demonstrated. A new approach of long-term dynamics analysis method has also been suggested. A successful classification of images was achieved after such simple enhancement tests. It has been discovered that, there were more active LULC change processes in the area in the first study period (1973 to 1986) than during the second study period (1986-2000). In the first period nearly half of the landscape underwent land cover change processes with more than 26% of the entire landscape experiencing forest or land degradation. In the second period the extent of the change process was limited to only 1/3 of the total area with a smaller amount of degradation processes than before. During the entire study period, agriculture was responsible for the loss of more than 4/5 of the total terrestrial productive ecosystem. More than 37.6% of the total park area has been experiencing this loss for the past 3 decades. Only 1/5 of this area has a chance to revive, the remaining has undergone a permanent degradation. Lake Abijjata lost half of its size during the past 30 years. In the Zeway-Awassa basin 750 km², 2428km² and 3575km² of terrestrial lands and water bodies are within a distance of 10km, 20km and 30km from IBAs respectively. There are ecologically important areas where two or more IBAs overlap. In areas where more than two to five IBAs overlap, up to 85km² of areas have been recently degraded. High livestock density is one of the reasons for degradation. Using a monthly MODIS data from 2000-2005 and a series of interpolation techniques, the productivity of the area as well as the standing biomass were estimated. Moreover, a new method of spatially accurate livestock density assessment was developed in this study. Only 0.3% of the park area is found to be suitable for productive livestock development but nearly all inhabitants think the area is suitable. Feed availability in ASLNP is scarce even during rainy seasons. Especially the open woodlands are subject to overgrazing. Such shortage forces the inhabitants to cut trees for charcoal making to buy animal feed and non-food consumables. While more than 95% of the inhabitants in the park expanded their agriculture lands, only 13.3% of the farmers managed to produce cereals for market. The application of low cost remote sensing and GIS methods provided ample information that enables to conclude that low productivity and household food insecurity are the main driving forces behind land cover changes that are negatively affecting the natural and semi-natural ecosystems in the central and southern Rift Valley of Ethiopia. The restoration of natural ecosystems or conservation of biodiversity can be achieved only if those driving forces are tackled sustainably

Modern Contraceptive Use and Associated Factors among Women within the Extended Postpartum Period in Gomma District,Jimma Zone, Oromia, Southwest Ethiopia,2022.

Background;- The extended postpartum period is a one-year time after giving birth during which women must have safe birth intervals. Many women’s are unaware that they are at risk for pregnancy during this time. As a result, many postpartum women did not begin using any form of contraception methods. As a result, there is a higher chance of an undesired pregnancy that leads mothers to pregnancy related complication. It is vital to have clear understanding of postpartum family planning services utilization and associated factors to achieve the desired health outcome for mother, neonate and children of the country. Objective; The aim of the study was to assess modern contraceptive use and associated factors among women’s within the extended postpartum period in Gomma, district, Jimma zone, Oromia, Ethiopia,2022. Method: Institutional based Quantitative cross sectional study design was conducted among 347 women within the extended postpartum period from May10 – June 20/2022. The study subject was selected by using systematic random sampling technique. Data was collected by using a structured and pretested interviewer administered questionnaire and the data was entered to Epi data version 4.6 and exported to SPSS version 25.0. Both bivariate and multivariate logistic regression model were performed to identify factors associated with outcome variable. Significance of association was decided by using the 95% Confidence level of AOR at p-value of <0.05. Result: Out of 347 sampled postpartum women, 337 of them responded with the response rate of 97.1%. The magnitude of postpartum contraceptive utilization was 30% (95% CI: 25.5-34.7). birth interval of ≤ 2 yrs (AOR =0.47, 95% CI: 0.19,0.90) was statistically negatively associated with modern PPFP use and Resumption of menses (AOR=4.34, 95% CI: 2.99-8.95), discussion with husband (AOR = 3.75, 95% CI: 1.76-7.97), ANC follow up (AOR=2.42,CI: 1.76-7.97), PNC follow up (AOR= 3.39, 95% CI: 1.73-6.68) and counseling during their child immunization (AOR=6.95, 95% CI:3.42-14.09) was statistically positively associated with postpartum modern contraceptive utilization among women within the extended postpartum period. Conclusion: The magnitude of postpartum modern contraceptive use during the extended postpartum period was low 30% (95% CI: 25.5- 34.7). Birth interval of ≤ 2 yrs, Resumption of menses, discussion with husband, ANC follow up, PNC follow up and counseling during their child immunization was statistically associated with postpartum contraceptive utilization among women within the extended postpartum period. Policy makers, program managers and health care providers need to focus on counseling and integration of postpartum family planning service and maternal and child health care service multiple contacts with health care professionals

Evaluation of the performance of Abbott Panbio™ COVID-19 antigen rapid diagnostic test for the detection of severe acute respiratory syndrome coronavirus 2 at Harar, Eastern Ethiopia

BackgroundRapid antigen tests can help in the effective isolation of symptomatic cases and the systematic tracing of close contacts. However, their reliability must be validated before implementing them widely.MethodsA cross-sectional study was conducted on 236 COVID-19-suspected patients visiting four different health institutions in Harari Regional State, Harar, Eastern Ethiopia, from June to July 2021. Two nasopharyngeal samples were collected and processed by the Panbio™ Ag-RDT kit and qRT-PCR. The collected data were analyzed using SPSS version 25.0.ResultsThe Panbio tests had a sensitivity of 77.5% (95% CI: 61.6–89.2%) and a specificity of 98.5% (95% CI: 95.6–99.7%). It also had a positive predictive value of 91.2% (95% CI: 76.9–96.9%), a negative predictive value of 95.5% (95% CI: 92.3–97.4%), and a kappa of 0.81 (95% CI: 0.7–0.9). The test had a sensitivity of 94.4%, 100%, 100%, and 90% in the samples collected from patients within the 1–5 days post-onset of COVID-19 signs and symptoms, of age group ≤18 years old, with cycle threshold values of &lt;20, and with household contact, respectively.ConclusionThis test can be used as point-of-care testing for the diagnosis of symptomatic patients with short clinical courses and contact with patients in households

Transition from long-term nonprogression to HIV-1 disease associated with escape from cellular immune control.

Transition from long-term nonprogressive infection to progressive HIV-1 disease presents an opportunity to investigate pathogenesis in a defined immunogenetic background. We studied a male long-term nonprogressor (LTNP) who remained asymptomatic and viremic and had normal CD4 T-cell counts without antiretroviral therapy for >18 years and then experienced a transition to disease progression. We analyzed the complete HIV-1 genomic RNA sequence from plasma and cellular immune responses to predefined human leukocyte antigen-matched autologous viral peptides spanning the viral genome, before and after progression. Serial viral sequences did not seem attenuated and consistently utilized coreceptor CCR5. LTNP status was associated with elongated V2 domains and broad low-level T-cell immune responses targeting several regions of the viral genome. The transition to progressive disease was associated with the acquisition of viral mutations conferring escape from CD8 T-cell responses. Multiple changes in HIV-1 sequence and loss of immune response over time most likely contributed to the transition from LTNP status to progressive disease. These data are relevant to vaccine design and identification of the correlates of protection from disease progression

Performance of Coffee Farmers’ Marketing Cooperatives in Yiragcheffe and Wonago Woredas, SNNPRS, Ethiopia

People form cooperatives to do something better than they could do individually or through a Cooperative form of business. Forming a cooperative will not automatically solve business problems faced by individual households. This is because cooperatives are subject to the same economic forces, legal restrictions and international relations that other business face. Cooperative members’ expectations about the types and quality of services that should be offered and their criteria for performance of these services have a major impact on the level of satisfaction or dissatisfaction felt. Members’ satisfaction on the benefits obtained by establishing cooperatives should be evaluated by the level of the deviation of service expectation from perceived service performance. Thus, cooperatives’ performance should be continuously checked against the level of members’ satisfaction. This study therefore, aims at assessing the performance of primary coffee marketing cooperatives and there by to identify factors that impede members’ satisfaction, and to evaluate the performance of coffee marketing cooperatives in the study area, Financial ratios were computed based on annual audit reports of the cooperatives. Here, efficiency ratios, income ratios and creditworthiness ratios were calculated as performance indicators. The result reveals that, almost all the coffee marketing cooperatives in the study areas were performing their business inefficiently. Probit regression model was also employed to identify factors influencing the members’ satisfaction, the adequacy and context of services rendered by the cooperatives, and the major services as function and of socio-economic and institutional explanatory variables. The model analysis revealed that, age, family size, terms of payment for red cherry and dry cherry were found to be statistically significant at significance level of 5%, 5% 1% and 5% respectively which influenced negatively except the terms of payment for dry cherry which influenced positively. The satisfaction of members’ of the coffee marketing cooperatives in the study areas was found to be poor with reference to the over all performance of the cooperatives

Genotypic and serotypic characterization of HIV in Ethiopia

The human immunodeficiency virus type I (HIV-1) is characterized by a high genomic heterogeneity. Different subtypes and inter-subtype recombinants have been identified in the HIV pandemic. The most precise and widely used method for subtype classification is based on molecular biology techniques; nucleotide sequencing of partial genomic fragments. However, since these methods are expensive, and demands high sample quality, it is not applicable for large epidemiological studies of subtype distributions. The aim of the present study was, to serologically and genotypically characterize HIV- 1 strains in Ethiopian patient materials. The pattern of serological reactivities of anti-HIV-1 antibodies to synthetic peptides of the five most prevalent subtypes, A-E, was studied by enzyme immunoassay (EIA). The peptides were 15 amino acids long and covered the middle part of the V3 region. The vast majority of the tested Ethiopian sera recognized the V3 peptide produced based on the local subtype C strain. Using substitution analogue peptides of the Ethiopian subtype C V3 sequence, it was found that the most essential amino acid residue for subtype C specific reactivity, was the glutamine (Q) within the GPGQ motif. Whereas, the GPG motif was responsible for the cross-reactivities with subtype B (MN) strain. Based on these observations, a method was developed in order to group HIV-1 infection into the major subtypes, A-E. The method was evaluated with a total of 106 sera obtained from Ethiopians, Swedes and Africans residing in Sweden. Swedish patients were mainly infected by subtype B and Ethiopian patients were mainly infected by subtype C. The serotyping results were compared with sequences of the V3 region. Using this method, 83 % of the sera were singly serotyped, and a 100 % concordance was found with V3 genotyping. To further evaluate the serotyping method, V3 and pl7 DNA sequences were obtained. The serotyping was done using a large sample size. The serotyping and genotyping were 74 % concordant. Discrepancy was found between V3 and pl7 DNA genotypes in some strains, suggesting possible recombinant strains. One of the putatively recombinant strains was from an Ethiopian patient. The presence of putative recombinant strains may partially explain the discordance between serotyping and genotyping. The putative recombinant strain identified from the Ethiopian patient was further investigated. To identify the pattern of recombination, and to indicate the recombination break points, a full length sequence was obtained. Using Recombination Identification Program (RIP), the recombination break point was suggested to be in the envelope region. The genetic organization of the Ethiopian HIV-1 subtype C strains was further investigated, by sequencing parts of the long terminal repeat (LTR), enhancer motif. The sequences were compared with Swedish and published sequence data. A sequence which appeared to be a third NF-kB binding site was identified in all Ethiopian sequences. This third NF-kB binding site was the first to be reported. However, the biological consequences of the additional site need to be investigated. Serotyping with short synthetic peptides and anti-HIV-1 antibodies could be valuable for seroepidemiological studies. Due to the dominance of the subtype C in Ethiopian HIV-1 epidemic, the existence of other subtypes and inter-subtype recombinant strains is still limited compared to some other African countries. Key words: HIV-1, V3, serotype, genotype, recombination ISBN-9 1 -628-2382-