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Article ; Online: Genotype Frequency of the Common TLR4 SNPs in a Kurdish Population: Global Reviews and Out-of-African Migrations.

Niranji, Sherko Subhan / Al-Jaf, Sirwan M A

2023 Volume 93, Issue 3, Page(s) 143–162

Abstract: Toll-like receptors (TLRs) are cellular innate immune receptors that explore microbial molecules. For instance, TLR4 can sense bacterial lipopolysaccharides, inducing cytokines and antimicrobial peptides against the bacteria. Single-nucleotide ... ...

Abstract	Toll-like receptors (TLRs) are cellular innate immune receptors that explore microbial molecules. For instance, TLR4 can sense bacterial lipopolysaccharides, inducing cytokines and antimicrobial peptides against the bacteria. Single-nucleotide polymorphisms (SNPs) in TLR4 are associated with diseases such as septic shock. Therefore, investigations of common SNPs may help explain the pathogenesis of diseases and various innate immune responses to infections. This study investigated genotypic frequencies of the two common TLR4 SNPs, Asp299Gly and Thr399Ile, in a Kurdish population using restriction length fragment polymorphisms (RFLPs). Global frequencies of both TLR4 SNPs in different populations of sub-Saharan Africa, North Africa, western Asia, Eurasia, and East Asia were also used to infer human migrations and past settlements. The RFLP data demonstrate that, in the Kurdish population, the genotypic frequencies of both SNPs are similar to Iranian or other West Asian populations, which in turn are comparable to Eurasian populations, suggesting past admixture due to migrations, population intermixing, and common ancestry. Globally, the frequencies of the homozygous wild-types of TLR4 variants are prevalent, but homozygous mutants are rare or lacking in almost all global populations. Frequencies of the heterozygotes varied among populations. For instance, in sub-Saharan Africa the frequency of the Asp299Gly SNP is higher than that of Thr399Ile, whereas in the Arabian Peninsula both SNPs are present at high frequencies. In contrast, East Asian populations lack or have very low frequencies of both TLR4 SNPs of interest. Moreover, co-segregation of the TLR4 SNPs is common in some populations, which may indicate important associations with certain diseases. Future studies are required to link the TLR4 SNPs with either resistance or susceptibility to diseases.
MeSH term(s)	Humans ; Polymorphism, Single Nucleotide/genetics ; Toll-Like Receptor 4/genetics ; Iran ; Genotype ; Homozygote
Chemical Substances	Toll-Like Receptor 4 ; TLR4 protein, human
Language	English
Publishing date	2023-09-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1116-2
ISSN	1534-6617 ; 0018-7143
ISSN (online)	1534-6617
ISSN	0018-7143
DOI	10.1353/hub.2021.0008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Comments on "Disease severity and efficacy of homologous vaccination among patients infected with SARS-CoV-2 Delta or Omicron VOCs, compared to unvaccinated using main biomarkers".

Muhammed, Omed A / Tawfeeq, Hiwa M / Al-Jaf, Sirwan M A / Niranji, Sherko S

Journal of medical virology

2023 Volume 95, Issue 5, Page(s) e28822

MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/prevention & control ; Patient Acuity ; Vaccination
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28822
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Article ; Online: Detection of SARS-CoV-2 Reinfections by Rapid Inexpensive Methods

Sirwan M.A. Al-jaf / Sherko S. Niranji

ARO-The Scientific Journal of Koya University, Vol 10, Iss

2022 Volume 1

Abstract: New SARS-CoV-2 infections are difficult to beverified, whether they are reinfections or persistent infections. The most prominent factors used for differentiating reinfections from persistent infections are whole-genome sequencing and phylogenetic ... ...

Abstract	New SARS-CoV-2 infections are difficult to beverified, whether they are reinfections or persistent infections. The most prominent factors used for differentiating reinfections from persistent infections are whole-genome sequencing and phylogenetic analyses that require time and funds, which may not be feasible in most developing countries. This study explores reinfections with COVID-19 that harbors D614G and N501Y mutations by rapid inexpensive methods. It exploits the previously developed rapid economic methods that identified both D614G and N501Y mutations in clinical samples using real-time reverse transcriptase polymerase chain reaction (rRT-PCR) probes and conventional PCR specific primers. In the present study, an immunocompetent patient has been found with a SARS-CoV-2 N501Y reinfection without comorbidities. According to the obtained results, this study suggests that the initial infection was due to a variant that contained only D614G mutation whereas the reinfection was potentially a result of alpha variant contained three mutations confirmed by DNA sequencing, including D614G, N501Y, and A570D mutations. These techniques will support rapid detection of SARS-CoV-2 reinfections through the identification of common spike mutations in the developing countries where sequencing tools are unavailable. Furthermore, seven cases of reinfections were also confirmed by these methods. These rapid methods can also be applied to large samples of reinfections that may increase our understanding epidemiology of the pandemic.
Keywords	Alpha variant ; Iraq ; Reinfections ; SARS- CoV-2 ; Agriculture ; S ; Technology ; T ; Science ; Q
Subject code	610
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Koya University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Association of Toll-like receptor-4 polymorphism with SARS CoV-2 infection in Kurdish Population.

Ali, Hussein N / Niranji, Sherko S / Al-Jaf, Sirwan M A

Human gene (Amsterdam, Netherlands)

2022 Volume 34, Page(s) 201115

Abstract: Genetic variations are critical for understanding clinical outcomes of infections including server acute respiratory syndrome coronavirus 2 (SARS CoV-2). The immunological reactions of human immune genes with SARS CoV-2 have been under investigation. ... ...

Abstract	Genetic variations are critical for understanding clinical outcomes of infections including server acute respiratory syndrome coronavirus 2 (SARS CoV-2). The immunological reactions of human immune genes with SARS CoV-2 have been under investigation. Toll-like receptors (TLRs), a group of proteins, are important for microbial detections including bacteria and viruses. TLR4 can sense both bacterial lipopolysaccharides (LPS) and endogenous oxidized phospholipids triggered by Covid-19 infection. Two TLR4 single nucleotide polymorphisms (SNPs), Asp299Gly and Thr399Ile have been linked to infectious diseases. No studies have focused on these SNPs in association with Covid-19. This study aims to reveal the association between Covid-19 infection with these SNPs by comparing a group of patients and a general population. Restriction fragment length polymorphisms (RFLP) were used to identify the TLR4 SNPs in both the general population (
Language	English
Publishing date	2022-10-04
Publishing country	Netherlands
Document type	Journal Article
ISSN	2773-0441
ISSN	2773-0441
DOI	10.1016/j.humgen.2022.201115
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Association of tumor necrosis factor alpha -308 single nucleotide polymorphism with SARS CoV-2 infection in an Iraqi Kurdish population.

Ali, Hussein N / Niranji, Sherko S / Al-Jaf, Sirwan M A

Journal of clinical laboratory analysis

2022 Volume 36, Issue 5, Page(s) e24400

Abstract: Uncovering risk factors playing roles in the severity of Coronavirus disease 2019 (Covid-19) are important for understanding pathoimmunology of the disease caused by severe acute respiratory syndrome Coronavirus 2 (SARS CoV-2). Genetic variations in ... ...

Abstract	Uncovering risk factors playing roles in the severity of Coronavirus disease 2019 (Covid-19) are important for understanding pathoimmunology of the disease caused by severe acute respiratory syndrome Coronavirus 2 (SARS CoV-2). Genetic variations in innate immune genes have been found to be associated with Covid-19 infections. A single-nucleotide polymorphism (SNP) in a promoter region of tumor necrosis factor alpha (TNF-α) gene, TNF-α -308G>A, increases expression of TNF-α protein against infectious diseases leading to immune dysregulations and organ damage. This study aims to discover associations between TNF-α -308G>A SNP and Covid-19 infection. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used for genotyping a general Kurdish population and Covid-19 patients. The homozygous mutant (AA) genotype was found to be rare in the current studied population. Interestingly, the heterozygous (GA) genotype was significantly (p value = 0.0342) higher in the Covid-19 patients than the general population. This suggests that TNF-α -308G>A SNP might be associated with Covid-19 infections. Further studies with larger sample sizes focusing on different ethnic populations are recommended.
MeSH term(s)	COVID-19/genetics ; Case-Control Studies ; Genetic Predisposition to Disease ; Genotype ; Humans ; Iraq ; Polymorphism, Single Nucleotide ; Tumor Necrosis Factor-alpha/genetics
Chemical Substances	TNF protein, human ; Tumor Necrosis Factor-alpha
Language	English
Publishing date	2022-04-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	645095-7
ISSN	1098-2825 ; 0887-8013
ISSN (online)	1098-2825
ISSN	0887-8013
DOI	10.1002/jcla.24400
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Article ; Online: Comments on 'Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2'.

Niranji, Sherko S / Al-Jaf, Sirwan M A

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2020 Volume 87, Page(s) 104661

MeSH term(s)	COVID-19 ; Humans ; Mutation ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; SARS-CoV-2
Language	English
Publishing date	2020-12-02
Publishing country	Netherlands
Document type	Journal Article ; Comment
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2020.104661
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Article: Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation.

Al-Jaf, Sirwan M A / Niranji, Sherko S / Mahmood, Zana H

Meta gene

2021 Volume 30, Page(s) 100950

Abstract: A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in the impact of this mutation on the virus's infectivity. Also, the whole genome ... ...

Abstract	A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in the impact of this mutation on the virus's infectivity. Also, the whole genome sequencings are expensive and time-consuming. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples. Both rRT and ARMS data showed G614 mutants indicated by the presence of HEX probe and 176 bp, respectively. Additionally, the results of the RFLP data and DNA sequencings confirmed the prevalence of the G614 mutants. These methods will be important, in epidemiological, reinfections and zoonotic aspects, through detecting the G614 mutant in retro-perspective samples to track its origins and future re-emergence of D614 wild type.
Language	English
Publishing date	2021-07-18
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2743632-9
ISSN	2214-5400
ISSN	2214-5400
DOI	10.1016/j.mgene.2021.100950
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Article ; Online: Rapid detection of SARS CoV-2 N501Y mutation in clinical samples

Al-Jaf, Sirwan M.A. / Niranji, Sherko Subhan

medRxiv

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) variants poses major threats in increasing infectivity, transmission, mortality of Coronavirus Disease 2019 (Covid-19). Additionally, SARS CoV-2 variants resist antibody neutralizations or may ... ...

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) variants poses major threats in increasing infectivity, transmission, mortality of Coronavirus Disease 2019 (Covid-19). Additionally, SARS CoV-2 variants resist antibody neutralizations or may abolish vaccine efficacies. Researches to develop economical and fast methods will support the developing or poor countries to challenge the Covid-19 pandemic via tracking common mutations that may help to deploy the vaccination programs and control the virus. Current study has developed a novel low-cost rapid technique, exploiting real time PCR probes and conventional PCR specific primers, to identify N501Y mutation, which was independently emerged in the UK, South African and Brazilian variants. Currently, these variants tend to spread to all over the world and seem to be more infectious, transmissible and fatal. This study helps tracking the N501Y mutation for understanding its clinical and epidemiological characteristics, in those countries where sequencing facilities are lacking or expensive. Further study should focus on other common mutations in the variants of concerns of SARS CoV-2.
Keywords	covid19
Language	English
Publishing date	2021-04-20
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.04.17.21255656
Database	COVID19

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Article ; Online: The Impact of SARS-CoV-2 Pandemic on Medical Students

Ahmed A. Mosa / Shah Vahel Ibrahim / Ibrahim A. Naqid / Dawan Jamal Hawezy / Sirwan M.A. Al-Jaf / Nawfal R. Hussein

Galician Medical Journal, Vol 30, Iss 1, Pp E202314-E

Knowledge, Attitudes, and Practices towards E-Learning: An Online Cross-Sectional Study in the Kurdistan Region, Iraq

2023 Volume 202314

Abstract: Background. After COVID-19 emergence, medical education witnessed a shift from face-to-face education to digital education, which inevitably affected medical students. Globally, due to the closure of schools and universities, medical education was ... ...

Abstract	Background. After COVID-19 emergence, medical education witnessed a shift from face-to-face education to digital education, which inevitably affected medical students. Globally, due to the closure of schools and universities, medical education was shifted to electronic learning (E-learning). This paper aimed to assess the effects of the COVID-19 pandemic on medical education and determine medical students’ knowledge, attitude, and practices towards E-learning in the Kurdistan Region of Iraq. Materials and Methods. An online cross-sectional study was conducted among 500 undergraduate students of seven medical colleges in the Kurdistan Region, Iraq, in November 2021, to assess their state during the COVID-19 pandemic and how this affected their education. Results. There were 50.6% of males and 49.4% of females. The mean age was 20.6 (± 1.5 SD) years. Approximately 17% of participants mentioned having financial issues, while 19.2% of students experienced health-related problems. As many as 67% of participants reported that the Internet quality was good or very good, whereas 46.8% of students disagreed that E-learning was a possible substitute for traditional learning. About two-thirds of participants agreed or were neutral that downloadable content was better than live content; however, only 19.2% of students agreed that E-learning could be used in the clinical aspect. A total of 52.2% of participants disagreed that E-testing could replace traditional learning methods. Surprisingly, 86.4% of students stated that they regularly used the Internet in their study. Conclusions. E-learning was the main adjustment made in the educational system, including medical education. The study concluded with insights into how different circumstances could have different consequences on the efficacy of medical education. E-learning showed effective results in continuing learning until the educational system switched to a blended system. Training programs for medical education personnel are vital in effective E-learning opportunities.
Keywords	covid-19 ; medical education ; medical students ; pandemic ; e-learning ; Medicine ; R
Subject code	370
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Ivano-Frankivsk National Medical University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Association of Apolipoprotein e polymorphism with SARS-CoV-2 infection.

Al-Jaf, Sirwan M A / Niranji, Sherko S / Ali, Hussein N / Mohammed, Omed A

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2021 Volume 95, Page(s) 105043

Abstract: Coronavirus 2019 (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The disease resulted in global morbidity and mortality that led to considering as pandemic. The human body response to COVID-19 ... ...

Abstract	Coronavirus 2019 (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The disease resulted in global morbidity and mortality that led to considering as pandemic. The human body response to COVID-19 infection was massively different from being asymptomatic to developing severe symptoms. Host genetic factors are thought to be one of the reasons for these disparities in body responses. Few studies have suggested that Apolipoprotein Epsilon (Apo E) is a candidate gene for playing roles in the development of the disease symptoms. This work aims to find an association between different Apo E genotypes and alleles to COVID-19 infection comparing a general population and a group of COVID-19 patients. For the first time, the results found that Apo E4 is associated with COVID-19 disease in a Kurdish population of Iraq. Further study is required to reveal this association in different ethnic backgrounds all over the world.
MeSH term(s)	Adult ; Aged ; Alleles ; Apolipoprotein E4/genetics ; Apolipoprotein E4/immunology ; Asymptomatic Diseases ; COVID-19/epidemiology ; COVID-19/genetics ; COVID-19/immunology ; COVID-19/virology ; Cohort Studies ; Ethnicity ; Female ; Gene Expression ; Gene Frequency ; Genetic Predisposition to Disease ; Humans ; Iraq/epidemiology ; Male ; Middle Aged ; Polymorphism, Genetic ; SARS-CoV-2/growth & development ; SARS-CoV-2/pathogenicity ; Severity of Illness Index
Chemical Substances	Apolipoprotein E4
Language	English
Publishing date	2021-08-19
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2021.105043
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