International Journal of Veterinary Science and Research
Pacific Biosciences has developed a platform that may sequence one molecule of DNA in a period vi... more Pacific Biosciences has developed a platform that may sequence one molecule of DNA in a period via the polymerization of that strand with one enzyme. Single-molecule real-time sequencing by Pacific BioSciences’ technology is one of the most widely utilized third-generation sequencing technologies. PacBio single-molecule real-time Sequencing uses the Zero-mode waveguide’s ingenuity to distinguish the best fluorescence signal from the stable fluorescent backgrounds generated by disorganized free-floating nucleotides. PacBio single-molecule real-time sequencing does not require PCR amplification, and the browse length is a hundred times longer than next-generation sequencing. It will only cover high-GC and high-repeat sections and is more accurate in quantifying low-frequency mutations. PacBio single-molecule real-time sequencing will have a relatively high error rate of 10%-15% (which is practically a standard flaw of existing single-molecule sequencing technology). In contrast to nex...
The Ethiopian government has several initiatives to expand and intensify the dairy industry; howe... more The Ethiopian government has several initiatives to expand and intensify the dairy industry; however, the risk of bovine tuberculosis (bTB) spread is a challenge. To assess the rate of expansion and risk factors for transmission of bTB within-herds, we carried out a repeated cross-sectional survey at two time points, 2016/17 and 2018, in three regional cities, namely, Gondar, Hawassa and Mekelle, representing the emerging dairy belts of Ethiopia. The total number of herds involved was 128, comprising an average of 2303 cattle in each round. The Single Intradermal Comparative Cervical Tuberculin (SICCT) test was used to identify reactor status and data on herd-level risk factors were collected using a structured questionnaire. In the first survey, the apparent prevalence of bTB, as measured by the SICCT test, was 4.5% (95% CI 3.7–5.4%) at the individual animal-level and 24% (95% CI 17.5–32%) at the herd-level. There was no statistically significant change in the overall apparent prev...
Background: In the Ethiopian dairy farming system, prevalence of zoonotic diseases such as bovine... more Background: In the Ethiopian dairy farming system, prevalence of zoonotic diseases such as bovine tuberculosis (bTB) is high in the cattle population. This, combined with some risky milk and meat consumption habits, such as raw milk and uninspected raw meat consumption, poses a considerable risk of zoonotic disease transmission. A survey was conducted to investigate milk and meat consumption patterns, and the level of exposure to urban and peri-urban dairy-keeping households for risks of zoonotic disease transmission.Methods: Data on milk and meat consumption behaviours and other socioeconomic and demographic variables were collected from 480 urban and peri-urban dairy farms randomly surveyed in major towns in Ethiopia (Mekele, Hawassa, and Gondar towns, Addis Ababa city, as well as five Oromia towns around Addis Ababa). Determinants of raw milk consumption associated with a number of demographic and socio-economic factors were analysed using a generalized ordered logistic model.Res...
BackgroundA Cross sectional study of Middle East Respiratory Syndrome Corona virus (MERS-CoV) in ... more BackgroundA Cross sectional study of Middle East Respiratory Syndrome Corona virus (MERS-CoV) in Camel was conducted between February 2018 to April 2019 in three selected sites of Amibara district of Afar region, Northeast Ethiopia. The study was aimed to observe the current sero-prevalence status of MERS-CoV, assess the presence of active cases through detection RNA Viral particle and investigate possible risk factors of MERS-CoV in camels. A total of 589 sera were collected and tested with indirect Enzyme linked ImmunoSorbent Assay (iELISA).ResultThe overall seroprevalance of MERS-CoV was 87.3% (n=514/589, 95% CI: 84.5-89.9). Association of different risk factors with seroprevalance revealed that origin (X2=13.39,P=0.001), sex (X2=4.5 P=0.034), age ((X2=185.7, P=0.001) season (X2=41.7, P=0.000) and reproduction status (X2=96.1, P=0.001) displayed a statistical significant difference among the groups (P<0.05) while herd size did not show a Significant difference among groups (p&...
Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest nati... more Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis (M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clona...
International Journal of Environmental Research and Public Health
Wastewater surveillance systems have become an important component of COVID-19 outbreak monitorin... more Wastewater surveillance systems have become an important component of COVID-19 outbreak monitoring in high-income settings. However, its use in most low-income settings has not been well-studied. This study assessed the feasibility and utility of wastewater surveillance system to monitor SARS-CoV-2 RNA in Addis Ababa, Ethiopia. The study was conducted at nine Membrane Bio-reactor (MBR) wastewater processing plants. The samples were collected in two separate time series. Wastewater samples and known leftover RT-PCR tested nasopharyngeal swabs were processed using two extraction protocols with different sample conditions. SARS-CoV-2 wastewater RT-PCR testing was conducted using RIDA GENE SARS-CoV-2 RUO protocol for wastewater SARS-CoV-2 RNA testing. Wastewater SARS-CoV-2 RNA RT-PCR protocol adaptation, optimization, and detection were conducted in an Addis Ababa, Ethiopia context. Samples collected during the first time series, when the national COVID-19 case load was low, were all ne...
Background Newcastle disease (ND) is a major infectious disease of poultry caused by a virulent s... more Background Newcastle disease (ND) is a major infectious disease of poultry caused by a virulent strain of Avian Paramyxovirus – 1. It is a major threat to the poultry industry in many countries of the world including Ethiopia. Newcastle Disease Virus (NDV) is an enveloped, non-segmented, single-stranded negative-sense RNA virus with a helical morphology whose genome has six open reading frames (ORF) which encode for the following proteins: nucleoprotein (NP), phosphoprotein (P), matrix protein (M), fusion protein (F), hemagglutinin-neuraminidase (HN) and RNA-dependent RNA polymerase (L). The aim of this study was to detect matrix gene (M-gene), for NDV by molecular tools and identify its risk factors in non-vaccinated village chicken in Central Rift Valley of Oromia, Ethiopia.Methods A total of 84 pooled in five swab samples from 420 cloacal and tracheal chickens were sampled and RNA was extracted from the 84 pooled samples to carry out real-time quantitative polymerase chain reacti...
International Journal of Veterinary Science and Research
Pacific Biosciences has developed a platform that may sequence one molecule of DNA in a period vi... more Pacific Biosciences has developed a platform that may sequence one molecule of DNA in a period via the polymerization of that strand with one enzyme. Single-molecule real-time sequencing by Pacific BioSciences’ technology is one of the most widely utilized third-generation sequencing technologies. PacBio single-molecule real-time Sequencing uses the Zero-mode waveguide’s ingenuity to distinguish the best fluorescence signal from the stable fluorescent backgrounds generated by disorganized free-floating nucleotides. PacBio single-molecule real-time sequencing does not require PCR amplification, and the browse length is a hundred times longer than next-generation sequencing. It will only cover high-GC and high-repeat sections and is more accurate in quantifying low-frequency mutations. PacBio single-molecule real-time sequencing will have a relatively high error rate of 10%-15% (which is practically a standard flaw of existing single-molecule sequencing technology). In contrast to nex...
The Ethiopian government has several initiatives to expand and intensify the dairy industry; howe... more The Ethiopian government has several initiatives to expand and intensify the dairy industry; however, the risk of bovine tuberculosis (bTB) spread is a challenge. To assess the rate of expansion and risk factors for transmission of bTB within-herds, we carried out a repeated cross-sectional survey at two time points, 2016/17 and 2018, in three regional cities, namely, Gondar, Hawassa and Mekelle, representing the emerging dairy belts of Ethiopia. The total number of herds involved was 128, comprising an average of 2303 cattle in each round. The Single Intradermal Comparative Cervical Tuberculin (SICCT) test was used to identify reactor status and data on herd-level risk factors were collected using a structured questionnaire. In the first survey, the apparent prevalence of bTB, as measured by the SICCT test, was 4.5% (95% CI 3.7–5.4%) at the individual animal-level and 24% (95% CI 17.5–32%) at the herd-level. There was no statistically significant change in the overall apparent prev...
Background: In the Ethiopian dairy farming system, prevalence of zoonotic diseases such as bovine... more Background: In the Ethiopian dairy farming system, prevalence of zoonotic diseases such as bovine tuberculosis (bTB) is high in the cattle population. This, combined with some risky milk and meat consumption habits, such as raw milk and uninspected raw meat consumption, poses a considerable risk of zoonotic disease transmission. A survey was conducted to investigate milk and meat consumption patterns, and the level of exposure to urban and peri-urban dairy-keeping households for risks of zoonotic disease transmission.Methods: Data on milk and meat consumption behaviours and other socioeconomic and demographic variables were collected from 480 urban and peri-urban dairy farms randomly surveyed in major towns in Ethiopia (Mekele, Hawassa, and Gondar towns, Addis Ababa city, as well as five Oromia towns around Addis Ababa). Determinants of raw milk consumption associated with a number of demographic and socio-economic factors were analysed using a generalized ordered logistic model.Res...
BackgroundA Cross sectional study of Middle East Respiratory Syndrome Corona virus (MERS-CoV) in ... more BackgroundA Cross sectional study of Middle East Respiratory Syndrome Corona virus (MERS-CoV) in Camel was conducted between February 2018 to April 2019 in three selected sites of Amibara district of Afar region, Northeast Ethiopia. The study was aimed to observe the current sero-prevalence status of MERS-CoV, assess the presence of active cases through detection RNA Viral particle and investigate possible risk factors of MERS-CoV in camels. A total of 589 sera were collected and tested with indirect Enzyme linked ImmunoSorbent Assay (iELISA).ResultThe overall seroprevalance of MERS-CoV was 87.3% (n=514/589, 95% CI: 84.5-89.9). Association of different risk factors with seroprevalance revealed that origin (X2=13.39,P=0.001), sex (X2=4.5 P=0.034), age ((X2=185.7, P=0.001) season (X2=41.7, P=0.000) and reproduction status (X2=96.1, P=0.001) displayed a statistical significant difference among the groups (P<0.05) while herd size did not show a Significant difference among groups (p&...
Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest nati... more Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis (M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clona...
International Journal of Environmental Research and Public Health
Wastewater surveillance systems have become an important component of COVID-19 outbreak monitorin... more Wastewater surveillance systems have become an important component of COVID-19 outbreak monitoring in high-income settings. However, its use in most low-income settings has not been well-studied. This study assessed the feasibility and utility of wastewater surveillance system to monitor SARS-CoV-2 RNA in Addis Ababa, Ethiopia. The study was conducted at nine Membrane Bio-reactor (MBR) wastewater processing plants. The samples were collected in two separate time series. Wastewater samples and known leftover RT-PCR tested nasopharyngeal swabs were processed using two extraction protocols with different sample conditions. SARS-CoV-2 wastewater RT-PCR testing was conducted using RIDA GENE SARS-CoV-2 RUO protocol for wastewater SARS-CoV-2 RNA testing. Wastewater SARS-CoV-2 RNA RT-PCR protocol adaptation, optimization, and detection were conducted in an Addis Ababa, Ethiopia context. Samples collected during the first time series, when the national COVID-19 case load was low, were all ne...
Background Newcastle disease (ND) is a major infectious disease of poultry caused by a virulent s... more Background Newcastle disease (ND) is a major infectious disease of poultry caused by a virulent strain of Avian Paramyxovirus – 1. It is a major threat to the poultry industry in many countries of the world including Ethiopia. Newcastle Disease Virus (NDV) is an enveloped, non-segmented, single-stranded negative-sense RNA virus with a helical morphology whose genome has six open reading frames (ORF) which encode for the following proteins: nucleoprotein (NP), phosphoprotein (P), matrix protein (M), fusion protein (F), hemagglutinin-neuraminidase (HN) and RNA-dependent RNA polymerase (L). The aim of this study was to detect matrix gene (M-gene), for NDV by molecular tools and identify its risk factors in non-vaccinated village chicken in Central Rift Valley of Oromia, Ethiopia.Methods A total of 84 pooled in five swab samples from 420 cloacal and tracheal chickens were sampled and RNA was extracted from the 84 pooled samples to carry out real-time quantitative polymerase chain reacti...
Uploads
Papers by Abde Aliy