Ali Hadi Abbas Abbas

The COVID-19 pandemic started in Wuhan China and rapidly transmitted worldwide, the illness is characterised by respiratory manifestations like coughing, breathing difficulties and pneumonia that could lead to death. Real-time whole genome sequencing of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) was adopted in many countries to track the infection dynamics and evolution of the virus. In parallel with the global efforts, genome sequencing trials were established in Iraq during the COVID-19 pandemic, however, this new approach has not been assessed yet. Therefore, for better readiness and improvement for future pandemics, here we obtained all genomes of SARS-CoV-2 virus from Iraq (182) that were deposited in National Center for Biotechnology Information (NCBI) during the period (2020–2023). Statistical analyses of sample size, distribution and other epidemiological parameters from associated metadata, as well as the quality of genome sequences were assessed. Our data analyses highlighted some drawbacks that could be improved, namely, that most genomic sequences (62%) were collected from only two cities, a low sample size was noticed and sequencing quality was inconsistent. There was a shortage and impairment of sequencing facilities especially those of the Ministry of Health. Consequently, genome sequencing should be achieved in centres that produce the best quality. The results revealed the importance of well-documented and high-quality sequences that represent many important cities in the country, which is crucial to draw a clear projection for health officials on infection dynamics and tracking viral evolution to help in taking successful steps towards infection control.

Marek’s disease (MD) is a highly infectious poultry illness with a tendency to form tumours in peripheral nerves and internal organs of affected birds. Tumours accompany MD, mostly caused by oncogenic Gallid alpha herpesvirus 2 (MD Herpes virus serotype I). Studies on avian tumours associated with MD infection are limited in Iraq. In the presented study, the positive samples of ocular tumour were 168 out of 282 MD positive samples, which accomplished in farm suffered from an unexpectedly high mortality rate. We investigated a rapidly developed tumour mass that was observed in an MD-vaccinated layer flock that showed obvious clinical signs of MD, accompanied by forming a small lump in one eye at age 21 weeks, which developed to a big lump at week 28 of age, leading to death. The diagnosis MD infection was confirmed by a Polymerase Chain Reaction (PCR) amplification of a specific region of the target gene meq of the causative agent, followed by Sanger sequencing and BLASTn search of the sequence against the NCBI nucleic acid database, resulted in Gallid alpha herpes virus 2 strain, and according to the phylogenetic analysis, the sequence from this study was uniquely clustered in its own branch in the tree. Histopathological examination of the ocular tumour core revealed aggregation of neoplastic cells and haemorrhage that replaced the normal eye tissue, as well as early tumour formation in internal organs such as the lung and liver. In addition, abnormal lesions are susceptible to tumours in the gizzard and spleen. To our knowledge, this is the first record of an aggressive MD virus infection-mediated ocular tumour in a layer flock in Al-Najaf province, Iraq.

Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.

AbstractThe PCR technique is a promising technique used to establish accurate identification methods to gain precise results. The incidence of yeast infections has increased dramatically coinciding with thebreakout of HIV infections. A quick and affordable diagnostic procedure is crutial in the quest to tacklesuch infections. In this study, a detailed diagnostic framework was designed to help in the rapididentification of pathogenicCandidaspecies. A sum of 17 Candidaspecies were involved in thisanalysis and a common conserved region of rRNA was detected to design primer pairs for in-silicoPCR. Restriction Fragment Length Polymorphism (RFLP) was used for species identification. One universal primer was designed to amplify the conserved region in all species, while two others werespecific to particular species. Results showed that the PCR-RFLP technique (by using the universalprimer No.1) identified 10 speciesClavispora lusitaniae, C. Cyberlindnera,C. asseri by unique restriction enzymeHinfI, C. carpophilaand C. quercitrusa usingHphI and,C. glabrata, Wickerhamomyces anomalus usingPhoI whileP. kudriavzevii andC. viswanathii usingBglI and BseGI respectively. Moreover,C. albicans PCR was identified by double restriction enzymesStuI and BspOI. The PCR-RFLP analysis has identified 7 species using primer pair No.2. These speciesareC. parapsilosis and Lodderomyces elongisporus by AatI and AcvI respectively. The Cleavage of PCR products using Bst4CI has identified four species (C. glabrata, C. lusitaniaeandC. tropicalis). C. dubliniensis was identified by double restriction enzymes (DraI+ ApoI). Meanwhile,C. orthopsilosiswas identified through DraI digestion of virtual PCR product (primer pair No.3). All together, these results showed that PCR-RFLP technique is an efficient and rapid method used to scrutinise accurateresults by computational based methods before being applied in the Lab. This study set up for a detailed guideline for an accurate, quick diagnostic procedure without any need for the sequencing step.K

Abstract African trypanosomiasis is a vector-borne disease of humans and livestock caused by African trypanosomes (Trypanosoma spp.). Survival in the vertebrate bloodstream depends on antigenic variation of Variant Surface Glycoproteins (VSGs) coating the parasite surface. In T. brucei, a model for antigenic variation, monoallelic VSG expression originates from dedicated VSG expression sites (VES). Trypanosoma brucei VES have a conserved structure consisting of a telomeric VSG locus downstream of unique, repeat sequences, and an independent promoter. Additional protein-coding sequences, known as “Expression Site Associated Genes (ESAGs)”, are also often present and are implicated in diverse, bloodstream-stage functions. Trypanosoma congolense is a related veterinary pathogen, also displaying VSG-mediated antigenic variation. A T. congolense VES has not been described, making it unclear if regulation of VSG expression is conserved between species. Here, we describe a conserved telomeric region associated with VSG loci from long-read DNA sequencing of two T. congolense strains, which consists of a distal repeat, conserved noncoding elements and other genes besides the VSG; although these are not orthologous to T. brucei ESAGs. Most conserved telomeric regions are associated with accessory minichromosomes, but the same structure may also be associated with megabase chromosomes. We propose that this region represents the T. congolense VES, and through comparison with T. brucei, we discuss the parallel evolution of antigenic switching mechanisms, and unique adaptation of the T. brucei VES for developmental regulation of bloodstream-stage genes. Hence, we provide a basis for understanding antigenic switching in T. congolense and the origins of the African trypanosome VES.

An awareness seminar was held at Youth education Center in Alghadeer Quarter, as a collaboration with the Najaf Governorate Youth Authority and the university's Women's Affairs Unit

The researcher was coauthored with well known researchers around the glob on a website on the global situation and antibiotic resistance of Salmonella bacterium

techniques used to determine the sequence of the nitrogenous bases of living organisms, or the abbreviation for decoding the genetic code, and the basics of each technique’s work, its benefits, and its uses in the biological and medical fields.

We hosted Prof. Dr. Jeffery Foster to give an online presentatoin on "Zoom" about the latest updates in infection and epidemiology of brucella with a global view.

Attending the international conference at University of Cambridge. Different talks and posters have been presented related to parasites .

Man research and posters have been presented with focus on genome sequencing of organisms and more specific to vertebrates and human genomic studies.