Egyptian Sequences Research Articles

Associative Genetic Diversity of Sarcocystis levinei Isolates across the Globe

Bubaline sarcocystosis, caused by Sarcocystis levinei, is worldwide in distribution. Yet, very limited reports are available across the globe on the phylogenetic aspects of this particular Sarcocystis spp. Virtually no literature is available on its molecular aspects from India. Thus, the present study was designed to phylogenetically characterize the various isolates of S. levinei based on 18S rRNA and cox 1 mitochondrial genes. A total of 11 isolates of S. levinei from Northern India were characterized for 18S rRNA (MG957189-MG957199) and cox 1 (MH255771-MH255781) genes. PCR products were cloned, sequenced, and compared with other sequences across the world. A phylogenetic tree was constructed based on the maximum likelihood (ML) method. Phylogenetic analysis placed S. levinei and S. cruzi into two monophyletic sister groups. An appreciable amount of genetic variability was noticed between various S. levinei sequences for both the gene loci. A total of three haplotypes were noticed for each gene. The generated sequences showed 99.8–100.0% and 99.7–100.0% nucleotide homologies within themselves with regard to the 18S rRNA and cox 1 genes, respectively. Few of the studied sequences showed marked similarity and closeness with the Egyptian sequences than their Indian counterparts. This is the first report of molecular characterization and sequence phylogenetic study of S. levinei from India.

Recent detection and Genotypic characterization of duck hepatitis virus A type 1and H5 avian influenza virus from ducks.

Objective: To identify some viruses affecting ducks by Serological and molecular studies.Design: Diagnostic study.Procedures: Twenty pooled liver samples were collected from ducklings less than 2 weeks showed nervous signs and high mortality suspected to be infected by duck hepatitis virus (DHV). All samples were inoculated in allantoic cavity of SPF embryonated chicken eggs (ECGs) for three successive passages. Isolates were serologically identified by agar gel precipitation (AGPT) and fluorescent antibody technique (FAT) by using DHAV-1 antibodies as well. Also, other 20 pooled lung and pancreas samples from ducks more than one month suspected to be infected by avian influenza virus (AIV) showed nervous signs; ataxia and torticolus. Suspected AIV samples were tested by reverse transcriptase polymerase chain reaction (RT-PCR) of H5 gene. Finally, sequencing and sequencing analysis of our RT-PCR products of DHAV-1 3D gene and AIV H5 gene with that published in GenBank.Results: Twelve out of 20 local isolates of DHAV-1 were positive in AGPT and 15 gave positive result in FAT. Twelve samples suspected to be AIV gave positive HA reaction. By RT-PCR 5 selected isolates of DHAV-1 and 5 out of 10 tested samples of AIV were positive and gave the expected bands. Our DHAV-1 isolates showed 100% identity to other Egyptian sequences from GenBank and H5 AIV showed 96-97% identity.Conclusion and clinical relevance: Both DHAV-1 and H5 AIV still in ducks could be identified by serological and molecular methods.

Lumpy skin disease in cattle in Sharkia, Egypt: epidemiological and genetic characterization of the virus.

Lumpy skin disease virus (LSDV) continues to threaten the cattle industry in Egypt. This survey investigated the epidemiological risk factors and the genetic characterization of circulating strains by partial sequencing of the P32 gene on cattle farms in the Sharkia Governorate, Egypt. Out of 600 cattle examined, morbidity, mortality, and case fatality were 31.2%, 1.8%, and 5.9%, respectively. Risk of LSD was higher among unvaccinated cattle kept outdoors compared to vaccinated cattle kept indoors, and the prevalence rates were statistically significantly different (P < 0.05). Regarding seasonal distribution, the highest number of cases was in June and July, and the lowest was in November. The P32 gene sequences showed that two LSDV isolates were 100% identical and 99.26% identical with 2017 Russian LSDV. Phylogenetic analysis revealed that two local isolates in this study were grouped together with other LSDVs from Russia (Saratov), Kenya, Greece, and Israel. The sequences in the study and other Egyptian sequences were grouped into two clusters with low genetic divergence, indicating that different strains are spreading in Egypt and that LSDV is more genetically related to sheep poxviruses than goat poxviruses. Our study confirms the necessity of evaluating the vaccination strategy adopted in Egypt, and sequence analysis based on the P32 gene is appropriate for genetic epidemiological studies of the local LSDVs.

Prévalence et facteurs de risque de la theilériose tropicale, et séquençage de l’agent pathogène causal &lt;em&gt;Theileria annulata&lt;/em&gt;, dans la région de Sétif (Algérie), avant et après la période d’infestation par les tiques

Pour déterminer la prévalence de l’infection par Theileria annulata et l’influence de certains facteurs de risque, une étude moléculaire a été menée dans la région de Sétif (Algérie). Au total, 134 échantillons sanguins de bovins provenant de 21 fermes ont été collectés deux fois, en avril et novembre 2015, avant et après la saison des vecteurs de tiques. La prévalence moléculaire de T. annulata a été de 25,4 % en avril et de 50 % en novembre, indiquant une augmentation significative (p &lt; 0,001) du nombre d’animaux porteurs asymptomatiques. La prévalence moléculaire a été significativement plus élevée que la prévalence sur frottis sanguins colorés au Giemsa pour les deux périodes. En avril, la race Fleckvieh a eu la prévalence moléculaire la plus faible mais cette prévalence a considérablement augmenté en novembre (p &lt; 0,001). Le type d’élevage et le sexe n’ont eu aucune influence sur la prévalence de T. annulata. Toutefois, le taux d’infection a augmenté de manière significative pendant la période d’infestation par les tiques, car les murs n’étaient pas crépis et présentaient des fissures (p &lt; 0,001). La séquence algérienne du gène Tams1 a été très similaire aux séquences mauritaniennes, tunisiennes et égyptiennes déjà connues.Temporaire Ouarda Ayadi

New insight into HCV E1/E2 region of genotype 4a.

IntroductionHepatitis C virus (HCV) genome contains two envelope proteins (E1 and E2) responsible for the virus entry into the cell. There is a substantial lack of sequences covering the full length of E1/E2 region for genotype 4. Our study aims at providing new sequences as well as characterizing the genetic divergence of the E1/E2 region of HCV 4a using our new sequences along with all publicly available datasets.MethodsThe genomic segments covering the whole E1/E2 region were isolated from Egyptian HCV patients and sequenced. The resulting 36 sequences 36 were analyzed using sequence analysis techniques to study variability within and among hosts in the same time point. Furthermore, previously published HCV E1/E2 sequence datasets for genotype 4a were retrieved and categorized according to the geographical location and date of isolation and were used for further analysis of variability among Egyptian over a period of 15 years, also compared with non-Egyptian sequences to figure out region-specific variability.ResultsPhylogenetic analysis of the new sequences has shown variability within the host and among different individuals in the same time point. Analysis of the 36 sequences along with the Egyptian sequences (254 sequences in E1 in the period from 1997 to 2010 and 8 E2 sequences in the period from 2006 to 2010) has shown temporal change over time. Analysis of the new HCV sequences with the non-Egyptian sequences (182 sequences in E1 and 155 sequences in the E2) has shown region specific variability. The molecular clock rate of E1 was estimated to be 5E-3 per site per year for Egyptian and 5.38E-3 for non-Egyptian. The clock rate of E2 was estimated to be 8.48E per site per year for Egyptian and 6.3E-3 for non-Egyptian.ConclusionThe results of this study support the high rate of evolution of the Egyptian HCV genotype 4a. It has also revealed significant level of genetic variability among sequences from different regions in the world.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-014-0231-y) contains supplementary material, which is available to authorized users.

Phylogenetic characterization of genotype 4 hepatitis C virus isolates from Argentina.

Among 114 patients infected with hepatitis C virus, three genotype 4 isolates, unusual in Argentina, were detected by phylogenetic analysis over different genomic regions. The patients were not related. One sample was associated with Egyptian sequences, and the others were associated with a Zairean isolate, a fact which reinforces the idea that they are from independent sources.