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Sudanese Phylogenetics

Mohamed E Ahmed, Bashir Salim, Martin P Grobusch, Imadeldin E Aradaib
BACKGROUND: Echinococcus granulosus sensu lato (s.l.) is the causative agent of cystic echinococcosis (CE), which is a cosmopolitan zoonotic parasitic disease infecting humans and a wide range of mammalian species including cattle. Currently, little information is available on the genetic diversity of Echinococcus species among livestock in Sudan. In the present study, fifty (n = 50) hydatid cysts were collected from cattle carcasses (one cyst sample per animal) at Al-kadarou slaughterhouse, Khartoum North, Sudan...
February 1, 2018: BMC Veterinary Research
Alassane Ouattara, Fidèle Tiendrébéogo, Pierre Lefeuvre, Murielle Hoareau, Sohini Claverie, Edgar Valentin Traoré, Nicolas Barro, Oumar Traoré, Arvind Varsani, Jean-Michel Lett
This is the first description of full genome sequences of chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus; family Geminiviridae) identified in papaya and tomato plants sampled in Burkina Faso. The CpCDV full genome sequences from papaya and tomato share the highest pairwise sequence identity (84% and 93.5%) with Sudanese isolates of the CpCDV-K and CpCDV-M strains, respectively. Based on the strain demarcation threshold (>94% identity) for mastreviruses, we propose two new strains, CpCDV-Q and CpCDV-R, identified in papaya and tomato, respectively...
June 2017: Archives of Virology
Mahmoud M Naguib, Dirk Höper, Abdel-Satar Arafa, Ahmed M Setta, Mohamed Abed, Isabella Monne, Martin Beer, Timm C Harder
Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry while different geno- and serotypes continue to circulate globally. Two infectious bronchitis viruses (IBV) were isolated from chickens with respiratory disease in Sudan. Sequence analysis of the hypervariable regions of the S1 gene revealed a close relation to the QX-like genotype which has not been detected in Sudan before. Whole genome analysis of IBV/Ck/Sudan/AR251-15/2014 isolate by next generation sequencing revealed a genome size of 27,646 nucleotides harbouring 13 open reading frames: 5'-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'...
December 2016: Infection, Genetics and Evolution
Adel Hussein Elduma, Mai Mohammed Adam Zein, Marie Karlsson, Isam M E Elkhidir, Heléne Norder
Few studies have reported sporadic hepatitis E virus (HEV) infections during non-outbreak periods in Africa. In this study, the prevalence of HEV infection in Sudan was investigated in 432 patients with acute hepatitis from 12 localities in North Kordofan, and from 152 patients involved in smaller outbreaks of hepatitis in the neighbouring Darfur. HEV infection was diagnosed in 147 (25%) patients: 98 from Kordofan and 49 from Darfur. The mortality was 10%; six of the patients who died from the infection were pregnant women...
October 6, 2016: Viruses
N A Elmardi, M A Bakheit, A I Khalafalla
A reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify 1412 bp of the fusion protein gene (F gene) of four Newcastle disease virus (NDV) isolates; two velogenic (TY-1/90 and DIK-90) and two lentogenic isolates (Dongla 88/1 and GD.S.1). Following sequencing, nucleotide sequences were annotated and 894 bp were compared phylogenetically with those from strains previously reported in the Sudan and the virus strains published on the GenBank. It could be demonstrated that TY-1/90 and DIK-90 strains belong to the genotype VI of NDV and are in close genetic relationship to sub- genotype VIb...
2016: Open Veterinary Journal
Robert E Tyx, Stephen B Stanfill, Lisa M Keong, Angel J Rivera, Glen A Satten, Clifford H Watson
The bacterial communities present in smokeless tobacco (ST) products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla...
2016: PloS One
Abdelmalik I Khalafalla, Ibrahim M El-Sabagh, Khalid A Al-Busada, Abdullah I Al-Mubarak, Yahia H Ali
BACKGROUND: Camel contagious ecthyma (CCE) is an important viral disease of camelids caused by a poxvirus of the genus parapoxvirus (PPV) of the family Poxviridae. The disease has been reported in west and east of the Sudan causing economical losses. However, the PPVs that cause the disease in camels of the Sudan have not yet subjected to genetic characterization. At present, the PPV that cause CCE cannot be properly classified because only few isolates that have been genetically analyzed...
August 12, 2015: Virology Journal
Charles E Wani, Ibrahim A Yousif, Muntasir E Ibrahim, Hassan H Musa
The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only...
2014: Genetics Research International
Mohamed A Soltan, Mohamed M Abd-Eldaim
Peste des petits ruminants (PPR) is an acute, highly contagious fatal disease of small ruminants characterized by high fever, ocular and nasal discharge, pneumonia, erosive stomatitis and severe enteritis that ultimately results in high mortalities. Peste des petits ruminants virus (PPRV) is widely distributed and endemic in several African, middle eastern and south Asian countries and it poses a threat to European countries. Egyptian veterinary medical authorities stated that Egypt is free from PPRV and the only measures for disease control are test and slaughter of infected population to maintain the free status...
December 2014: Infection, Genetics and Evolution
Tsegaw Fentie, Alireza Heidari, Roberta Aiello, Tesfu Kassa, Ilaria Capua, Giovanni Cattoli, Mesfin Sahle
Newcastle disease (ND) is a highly contagious disease that affects many species of birds and causes significant economic losses to the poultry industry worldwide. Fifteen Newcastle disease virus (NDV) isolates obtained from rural chickens in northwest Ethiopia in 2011 and 2012 were characterized genotypically. The main functional region of the F gene was amplified and sequenced (260 nucleotides). Among the Ethiopian NDV isolates, 2 isolates had the virulent motif (112)R-R-Q-K-R-F(117) at the cleavage site of the fusion protein while 13 isolates contained the lentogenic motif (112)G-G/R-Q-G-R-L(117)...
February 2014: Tropical Animal Health and Production
Mohamed E Ahmed, Kamal H Eltom, Nasreen O Musa, Ibtisam A Ali, Fatima M Elamin, Martin P Grobusch, Imadeldin E Aradaib
BACKGROUND: Echinococcus granulosus (EG) complex, the cause of cystic echinococcosis (CE), infects humans and several other animal species worldwide and hence the disease is of public health importance. Ten genetic variants, or genotypes designated as (G1-G10), are distributed worldwide based on genetic diversity. The objective of this study was to provide some sequence data and phylogeny of EG isolates recovered from the Sudanese one-humped camel (Camelus dromedaries). Fifty samples of hydatid cysts were collected from the one- humped camels (Camelus dromedaries) at Taboul slaughter house, central Sudan...
June 25, 2013: BMC Veterinary Research
Imadeldin E Aradaib, Bobbie R Erickson, Mubarak S Karsany, Marina L Khristova, Rehab M Elageb, Mohamed E H Mohamed, Stuart T Nichol
BACKGROUND: Crimean-Congo hemorrhagic fever (CCHF) activity has recently been detected in the Kordufan region of Sudan. Since 2008, several sporadic cases and nosocomial outbreaks associated with high case-fatality have been reported in villages and rural hospitals in the region. PRINCIPAL FINDINGS: In the present study, we describe a cluster of cases occurring in June 2009 in Dunkop village, Abyei District, South Kordufan, Sudan. Seven CCHF cases were involved in the outbreak; however, clinical specimens could be collected from only two patients, both of whom were confirmed as acute CCHF cases using CCHF-specific reverse transcriptase polymerase chain reaction (RT-PCR)...
2011: PLoS Neglected Tropical Diseases
Bashir Salim, Mohammed A Bakheit, Sir Elkhatim Salih, Joseph Kamau, Ichiro Nakamura, Ryo Nakao, Chihiro Sugimoto
BACKGROUND: In this paper, we report an outbreak of bovine trypanosomiasis in Kurmuk District, Blue Nile State, Sudan that involved an infection with four Trypanosoma species in cattle. The outbreak occurred in June 2010 when indigenous cattle, mainly Kenana and Fulani breed types, crossed the national Sudanese border to Ethiopia and returned. A veterinarian was notified of massive deaths in the cattle populations that recently came from Ethiopia. All animals involved in the outbreak were from the nomadic Fulani group and resident local cattle were not infected and no death has been reported among them...
2011: Parasites & Vectors
Imen Khlif Amouri, Habib Kharmachi, Ahlem Djebbi, Mohamed Saadi, Nahed Hogga, Lotfi Ben Zakour, Abdeljelil Ghram
In an attempt to explain temporal and geographical rabies incidence fluctuations in Tunisia, a molecular epidemiological study of rabies virus (RV) was carried out. A panel of RV isolates from dogs, collected between 1992 and 2003, from different regions in Tunisia have been analysed by direct sequencing of PCR-amplified products coding for the nucleoprotein gene. New sequences have been compared to prototype sequences of Lyssavirus species and nine lineages of species 1. All Tunisian isolates belonged to species rabies virus and segregated into two rabies lineages geographically distinct: NCS lineage characterizing Northeast, Central and Northern areas of the country and NW lineage more restricted to the North-Western regions...
June 2011: Virus Research
M Habiela, N P Ferris, G H Hutchings, J Wadsworth, S M Reid, M Madi, K Ebert, K J Sumption, N J Knowles, D P King, D J Paton
The aim of this study was to characterize foot-and-mouth disease (FMD) viruses collected between 2004 and 2008 from Sudan, a country where FMD is endemic. Using virus isolation and antigen ELISA, three FMD virus serotypes (O, A and SAT2) were detected in 24 samples that were submitted to the FAO World Reference Laboratory for FMD. Pan-serotypic real-time RT-PCR assays targeting the 5' untranslated region (5'UTR) and 3D genes of FMD virus were also used to contribute to the laboratory diagnosis of these cases...
October 2010: Transboundary and Emerging Diseases
E Gadisa, T Kuru, A Genet, H Engers, A Aseffa, L Gedamu
In Ethiopia, visceral leishmaniasis (VL) is an increasing public health concern. Recently, a new outbreak of VL claimed the lives of hundreds of Ethiopians. Mapping its distribution and the identification of the causative Leishmania species is important for proper use of resources and for control planning. The choice of appropriate typing technique is the key for determining the infecting species. Here we compared three deoxyribonucleic acid (DNA) based markers. We used, for the first time, cpbE and cpbF (cpbE/F) PCR-RFLP and demonstrated that it clearly differentiates Leishmania donovani from Leishmania infantum...
October 2010: Experimental Parasitology
D A Marston, L M McElhinney, Y H Ali, K S Intisar, S M Ho, C Freuling, T Müller, A R Fooks
Rabies is endemic in Sudan and remains a continual threat to public health as transmission to humans is principally dog-mediated. Additionally, large-scale losses of livestock occur each year causing economic and social dilemmas. In this study, we analysed a cohort of 143 rabies viruses circulating in Sudan collected from 10 different animal species between 1992 and 2006. Partial nucleoprotein sequence data (400 bp) were obtained and compared to available sequence data of African classical rabies virus (RABV) isolates...
November 2009: Virus Research
J M Mwacharo, K Nomura, H Hanada, H Jianlin, O Hanotte, T Amano
In this study, 30 microsatellite markers recommended by the International Society for Animal Genetics and the Food and Agriculture Organization were used to determine the extent of genetic differentiation and phylogenetic relationships among indigenous chicken populations sampled in Kenya, Uganda, Ethiopia and Sudan. Genetic differentiation (F(ST)) and chord genetic distances (D(C)) indicated that the indigenous chickens were genetically related but distinct from commercial broiler and egg layer lines. Genetic divergence among the indigenous chickens determined using the Mantel test was significantly influenced (P < 0...
October 2007: Animal Genetics
Khalid Dafaallah Awadelkarim, Gitana Aceto, Serena Veschi, Ahmed Elhaj, Annalisa Morgano, Ahmed Abdalla Mohamedani, Elgaylani Abdalla Eltayeb, Dafaallah Abuidris, Mario Di Gioacchino, Pasquale Battista, Fabio Verginelli, Alessandro Cama, Nasr Eldin Elwali, Renato Mariani-Costantini
The etiology of breast cancer in Africa is scarcely investigated. Breast cancer was responsible for 456/2,233 cancer patients (20.4%) ascertained between 1999 and 2004 at Gezira University, Central Sudan. Male breast cancer accounted for 16/456 patients (3.5%), 275/440 female patients (62.5%) were premenopausal and 150/440 cases (34%) occurred in women with > or =5 childbirths. We characterized for germline BRCA1/2 mutations a one-year series of patients (34 females, 1 male) selected by diagnosis within age 40 years or male gender...
April 2007: Breast Cancer Research and Treatment
Katrin Kuhls, Isabel L Mauricio, Francine Pratlong, Wolfgang Presber, Gabriele Schönian
To understand phylogenetic relationships of species and strains within the Leishmania donovani complex, we have analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 27 Leishmania infantum, 2 Leishmania chagasi, 18 L. donovani and 5 Leishmania archibaldi strains of different zymodemes and geographical origin. Eight ITS sequence types were found. All detected sequence variation within ITS1 and ITS2 was based on 12 polymorphic microsatellites. The L. infantum strains from the Mediterranean region, China and L...
August 2005: Microbes and Infection
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