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Article: In Silico Evaluation of SARS-CoV-2 K417N, L452R, and E484K Detection Assays Against Omicron Variants.

Sayan, Murat / Arikan, Ayse / Isbilen, Murat

2023 Volume 46, Issue 2, Page(s) 133–140

Abstract: The study's objective was to assess whether the performance of the DIAGNOVITAL SARS-CoV-2 Mutation Detection Assays is affected by Omicron mutations. In silico evaluation of 67,717 Variant of Concern, Variant of Interest sequences and 6,612 sequences of ... ...

Abstract	The study's objective was to assess whether the performance of the DIAGNOVITAL SARS-CoV-2 Mutation Detection Assays is affected by Omicron mutations. In silico evaluation of 67,717 Variant of Concern, Variant of Interest sequences and 6,612 sequences of the Omicron variants involving BA1., BA2., BA3 sub-lineages downloaded from the GISAID database by 17 December 2021, were performed. The sequences were aligned according to the reference genome MN908947.3 using MAFFT multiple sequence alignment software version 7. Our findings showed that among 6,612 Omicron, 41 Spike gene mutations with a frequency of ≥70% were identified. Some of the Omicron mutations (R408S, N440K, G446S, Q493S, Q498R) could affect the diagnostic performance of K417N, L452R, and E484K assays against the Omicron sub-lineages. However, L452R and K417N mutation tests allow differentiation of the Delta and Omicron variants mutation profile. The COVID-19 pandemic lasted longer than expected, and the rapid modification of diagnostic kits seems necessary to combat the pandemic.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; Pandemics ; Mutation
Language	English
Publishing date	2023-05-29
Publishing country	Italy
Document type	Journal Article
ZDB-ID	756168-4
ISSN	1121-7138 ; 0391-5352
ISSN	1121-7138 ; 0391-5352
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Article ; Online: Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database.

Sayan, Murat / Arikan, Ayse / Isbilen, Murat

Journal of comparative effectiveness research

2022 Volume 11, Issue 3, Page(s) 157–167

Abstract: Aims: ...

Abstract	Aims:
MeSH term(s)	Antiviral Agents/therapeutic use ; COVID-19 ; Humans ; Phylogeny ; SARS-CoV-2
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2022-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2669725-7
ISSN	2042-6313 ; 2042-6305
ISSN (online)	2042-6313
ISSN	2042-6305
DOI	10.2217/cer-2021-0208
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Article: Investigation of SARS-CoV-2 Variants and Their Effect on SARS-CoV-2 Monoclonal Antibodies, Convalescent and Vaccine Plasma by a Novel Web Tool.

Arikan, Ayse / Sayan, Murat

Diagnostics (Basel, Switzerland)

2022 Volume 12, Issue 11

Abstract: 1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against ... ...

Abstract	(1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against monoclonal antibodies, convalescent, and vaccine plasma. (2) Methods: Strains isolated from COVID-19 cases in Turkey in April and September 2021 were involved. Illuma Nextera XT was processed for NGS, followed by virtual phenotyping (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). (3) Results: Among 211 strains, 79% were SARS-CoV-2 variants. B.1.1.7 (Alpha) was the most dominant, followed by B.1.617.2 (Delta), B.1.351 (Beta), and B.1.525 (Eta). Alpha and Delta were less susceptible to Etesevimab-Sotrovimab and Bamlanivimab-Etesevimab, respectively. Reduced efficacy was observed for convalescent plasma in Beta and Delta; AstraZeneca, Comirnaty plus AstraZeneca in Alpha; Comirnaty, Moderna, Novovax in Beta; Comirnaty in Delta. (4) Conclusion: CoV-RDB analysis is an efficient, rapid, and helpful web tool for SARS-CoV-2 variant detection and susceptibility analysis.
Language	English
Publishing date	2022-11-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662336-5
ISSN	2075-4418
ISSN	2075-4418
DOI	10.3390/diagnostics12112869
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Article ; Online: Molecular Epidemiology of SARS-CoV-2 Omicron Sub-Lineages Isolated from Turkish Patients Infected with COVID-19.

Sayan, Murat / Arikan, Ayse / Sanlidag, Erdal

Viruses

2023 Volume 15, Issue 5

Abstract: Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral ... ...

Abstract	Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford University Coronavirus Antiviral & Resistance Database online tool was used for variant analyses of the strains uploaded to GISAID as Omicron (
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Molecular Epidemiology ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; RNA-Dependent RNA Polymerase
Chemical Substances	ensitrelvir (PX665RAA3H) ; Antiviral Agents ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2023-04-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15051066
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Article: Circulating Dynamics of SARS-CoV-2 Variants between April 2021 and February 2022 in Turkey.

Sayan, Murat / Arikan, Ayse / Isbilen, Murat

The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale

2022 Volume 2022, Page(s) 4677720

Abstract: The diagnosis of new variants and monitoring their potential effects on diagnosis, therapeutics, and vaccines by genomic sequencing is essential to manage global public crises. In the current study, spike-genome next-generation sequencing was generated ... ...

Abstract	The diagnosis of new variants and monitoring their potential effects on diagnosis, therapeutics, and vaccines by genomic sequencing is essential to manage global public crises. In the current study, spike-genome next-generation sequencing was generated from 492 SARS-CoV-2 isolates to evaluate the mutations in Turkey from April 2021 to February 2022. The variant analysis was performed using (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). We revealed that the lineages Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), Eta (B.1.525), variant of interest (VOI), lota (B.1.526), Zeta (P.2), Omicron (B.1.1.529), and Omicron BA.1 (B.1.1.529.1) were in the circulation in Turkey during the given period. The most common lineages were B.1.1.7, B.1.617.2, B.1.1.529, and B.1.1.529.1 SARS-CoV-2 variant circulation in Turkey seems highly heterogenetic; however, quite similar to the global epidemiologic analysis. The existence of globally circulating variants in the same chronological order in Turkey can be a guide for precautions, treatment, and vaccine options to be taken in the future.
Language	English
Publishing date	2022-10-15
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	1057056-1
ISSN	1712-9532 ; 1180-2332
ISSN	1712-9532 ; 1180-2332
DOI	10.1155/2022/4677720
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Article ; Online: Dynamics of Rilpivirine Resistance-Associated Mutation: E138 in Reverse Transcriptase among Antiretroviral-Naive HIV-1-Infected Individuals in Turkey.

Sayan, Murat / Sultanoglu, Nazife / Sanlidag, Tamer

AIDS research and human retroviruses

2023 Volume 39, Issue 2, Page(s) 84–90

Abstract: Rilpivirine, one of the non-nucleoside reverse transcriptase inhibitors class anti-HIV agents, is used as an alternative drug to treat HIV-1-positive individuals according to current antiretroviral therapy (ART) guidelines. Mutation in the position E138 ... ...

Abstract	Rilpivirine, one of the non-nucleoside reverse transcriptase inhibitors class anti-HIV agents, is used as an alternative drug to treat HIV-1-positive individuals according to current antiretroviral therapy (ART) guidelines. Mutation in the position E138 in HIV-1 reverse transcriptase (RT) leads to resistance to rilpivirine, alone reducing its susceptibility two to threefolds. The main aim of this study was to determine the dynamics of E138 mutation in the RT domain of the HIV-1 pol gene; in 6398 newly diagnosed and treatment-naive individuals in Turkey from 2013 to 2021. Rilpivirine-associated mutations were found among 424 (6.6%) out of 6398. Individuals with the E138 mutation had significantly higher HIV-1 RNA load than individuals without the E138 mutation (
MeSH term(s)	Humans ; Anti-HIV Agents/pharmacology ; Anti-HIV Agents/therapeutic use ; Anti-Retroviral Agents/therapeutic use ; Drug Resistance, Viral/genetics ; HIV Infections/drug therapy ; HIV Infections/epidemiology ; HIV Seropositivity/drug therapy ; HIV-1/genetics ; Mutation ; Reverse Transcriptase Inhibitors/pharmacology ; Reverse Transcriptase Inhibitors/therapeutic use ; Rilpivirine/pharmacology ; Rilpivirine/therapeutic use ; Turkey
Chemical Substances	Anti-HIV Agents ; Anti-Retroviral Agents ; Reverse Transcriptase Inhibitors ; Rilpivirine (FI96A8X663) ; reverse transcriptase, Human immunodeficiency virus 1 (EC 2.7.7.-)
Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/AID.2022.0065
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Zs.A 1928: Show issues

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Article ; Online: Molecular Epidemiology of HIV-1 Subtypes and Primary Antiretroviral Resistance Profiles in Northern Cyprus: First Data Series.

Guler, Emrah / Arikan, Ayse / Sultanoglu, Nazife / Suer, Kaya / Sanlidag, Tamer / Sayan, Murat

AIDS research and human retroviruses

2024

Abstract: The distribution of human immunodeficiency virus-1 (HIV-1) subtypes indicates difference from region to region and in risk groups acquiring the disease worldwide. Although subtype C is more in terms of total cases, subtype B is dominant in certain ... ...

Abstract	The distribution of human immunodeficiency virus-1 (HIV-1) subtypes indicates difference from region to region and in risk groups acquiring the disease worldwide. Although subtype C is more in terms of total cases, subtype B is dominant in certain regions, especially in western and central Europe. Molecular epidemiological studies are essential for the control, effective treatment, and understanding in transmission routes of HIV-1 infection. This study aims to determine the molecular epidemiology and antiretroviral drug resistance profiles of HIV-1 in northern Cyprus. The study involved 71 naive HIV-positive patients diagnosed in northern Cyprus between 2016 and 2022. HIV-1 subtypes and circulating recombinant forms (CRFs) were identified by phylogenetic analysis (neighbor-joining method) of
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/AID.2023.0021
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Article: A felső végtag antropometriájának és subcutan zsírszövetének a carpalis alagút szindrómával való összefüggése.

Darol, Elif Sarica / Çiçekli, Esen / Sayan, Saadet / Kotan, Dilcan / Alemdar, Murat

Ideggyogyaszati szemle

2024 Volume 77, Issue 1-2, Page(s) 5–12

Abstract: Background and purpose: ... Body mass index (BMI) is positively correlated with the frequency of carpal tunnel syndrome (CTS). However, there are different types of obesity, and the localization of adipose tissue differs between the genders. In this ... ...

Title translation	Association of upper extremity anthropometry and subcutaneus adipose tissue with carpal tunnel syndrome.
Abstract	Background and purpose: Body mass index (BMI) is positively correlated with the frequency of carpal tunnel syndrome (CTS). However, there are different types of obesity, and the localization of adipose tissue differs between the genders. In this study, we purposed to investigate whether there was an association between the amount of local adipose tissue thickness and anthropometry in upper extremity with the presence and/or electrophysiological severity of CTS on both genders. . Methods: Our study included 150 patients who were diagnosed with CTS clinically and electrophysiologically and 165 healthy controls. The biceps and triceps skinfold thickness, the diameters of the wrist and metacarpal joints, and the upper arm circumferences over the belly of the biceps muscle were measured by using skinfold caliper and measuring cylinder. All data were analyzed by using the Statistics Open For All package (SofaStats) programme. To detect the role of anthropometric indexes, we used multivariable multinomial logistic regression models. . Results: We revealed that BMI, biceps and triceps adipose tissue thicknesses were higher in females and also in patients with CTS. There was a positive correlation between electrophysiological grades of CTS and BMI with logistic regression analyzes. The mean Wrist circumference/Metacarpopharengeal Circumference ratio and biceps circumference were higher in moderate CTS groups. Metacarpofarengeal circumference was smaller in mild and moderate CTS cases compared to healthy ones. . Conclusion: We suggest that the differences between the anatomical bone structure and local adiposity between the genders may play an important role in the occurrence of CTS. Moreover, the structures of proximal muscle groups and distal metacarpal joints may contribute both to the development and severity of CTS. .
MeSH term(s)	Humans ; Female ; Male ; Carpal Tunnel Syndrome/diagnosis ; Anthropometry ; Wrist/anatomy & histology ; Body Mass Index ; Obesity ; Adipose Tissue
Language	Hungarian
Publishing date	2024-02-06
Publishing country	Hungary
Document type	English Abstract ; Journal Article
ZDB-ID	2240317-6
ISSN	0019-1442
ISSN	0019-1442
DOI	10.18071/isz.77.0005
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Article ; Online: Evaluation of lateral flow and ELISA techniques for detecting IgG and IgM antibodies in COVID-19 cases in Türkiye.

Arikan, Ayse / Doluca, Osman / Akhan, Sila / Sanlidag, Tamer / Sayan, Murat

Eastern Mediterranean health journal = La revue de sante de la Mediterranee orientale = al-Majallah al-sihhiyah li-sharq al-mutawassit

2023 Volume 29, Issue 2, Page(s) 91–99

Abstract: Background: Antibody testing can complement molecular assays for detecting COVID-19.: Aims: We evaluated the concurrence between lateral flow assay and enzyme-linked immunosorbent assay (ELISA) for the detection of antibodies in severe acute ... ...

Abstract	Background: Antibody testing can complement molecular assays for detecting COVID-19. Aims: We evaluated the concurrence between lateral flow assay and enzyme-linked immunosorbent assay (ELISA) for the detection of antibodies in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: The study was conducted at Kocaeli University, Türkiye. We used a lateral flow assay and ELISA to test serum samples from COVID-19 cases, confirmed by polymerase chain reaction assays (study group) and pre-pandemic stored serum samples (control group). We used Deming regression to evaluate the antibody measurements. Results: The study group included 100 COVID-19 cases, and the control group included pre-pandemic samples from 156 individuals. The lateral flow assay detected immunoglobulin M (IgM) and G (IgG) antibodies in 35 and 37 study group samples. ELISA detected IgM nucleocapsid (N) antibodies in 18 samples, and IgG (N) and IgG spike 1 (S1) antibodies in 31 and 29 samples, respectively. None of the techniques detected antibodies in the control samples. Strong correlations were found between lateral flow IgG (N+ receptor-binding domain + S1) and ELISA IgG (S) (r = 0.93, P < 0.01) and ELISA IgG (N) (r = 0.81, P < 0.01). Weaker correlations were seen between ELISA IgG S and IgG N (r = 0.79, P < 0.01) and lateral flow assay and ELISA IgM (N) (r = 0.70, P < 0.01). Conclusion: Lateral flow assay and ELISA techniques gave consistent results for IgG/IgM antibody measurements towards spike and nucleocapsid proteins, suggesting that both methods can be used to detect COVID-19 where access to molecular test kits is difficult.
MeSH term(s)	Humans ; COVID-19/diagnosis ; SARS-CoV-2 ; Enzyme-Linked Immunosorbent Assay ; Immunoglobulin M ; Immunoglobulin G
Chemical Substances	Immunoglobulin M ; Immunoglobulin G
Language	English
Publishing date	2023-02-26
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	1291071-5
ISSN	1687-1634 ; 1020-3397
ISSN (online)	1687-1634
ISSN	1020-3397
DOI	10.26719/emhj.23.011
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Zs.A 4388: Show issues

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Article ; Online: Evaluation of Point-of-care and Traditional ELISA Techniques for the Detection of Anti-SARS-CoV-2 IgG Antibodies in Individuals Vaccinated Against COVID-19

Müge TOYGAR DENİZ / Murat SAYAN / Sıla AKHAN / Ebru KARACA

Mediterranean Journal of Infection, Microbes and Antimicrobials, Vol 12, Iss

2023 Volume 1

Abstract: Introduction: Coronavirus disease-2019 (COVID-19) has affected more than 676 million people till date, and 6,881,955 people have died from the disease as of March 28, 2023. Understanding the immunopathogenesis of the disease has led to more vaccine ... ...

Abstract	Introduction: Coronavirus disease-2019 (COVID-19) has affected more than 676 million people till date, and 6,881,955 people have died from the disease as of March 28, 2023. Understanding the immunopathogenesis of the disease has led to more vaccine studies. The Comirnaty and CoronaVac vaccines are used in our country. The role of serology tests in the interpretation of protective and sustained immunity remains controversial after vaccines. However, serological testing is part of epidemiology and is essential for understanding the immunity against Severe acute respiratory syndrome-Coronavirus-2. We aimed to determine the antibody titers after vaccination and its effect on immunity, which could lead to new studies. Materials and Methods: Two traditional enzyme-linked immunosorbent assay (ELISA) techniques (Euroimmune and Genzbio Covel) and one point-of-care (POC) method (Genz-Pro) were used in our study for detecting antibodies in vaccinated individuals. Results: A total of 84 individuals were included in our study. The results obtained using the Genz-Pro test were evaluated according to the vaccine status; the positive antibody detection rate was significantly higher in Comirnaty-vaccinated patients than in CoronaVac-vaccinated individuals. The Spearman’s correlation coefficient demonstrated a positive correlation between the two ELISA techniques. Conclusion: The POC ELISA can quantify IgG seroconversion after COVID-19 vaccination with rapid and multiple measurements without sample accumulation. Thus, the POC ELISA can be used in COVID-19 services and outpatient clinics during post-vaccination follow-up to determine the performance of vaccines.
Keywords	point-of-care systems ; covid-19 testing ; antibodies ; serologic tests ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Subject code	630
Language	Turkish
Publishing date	2023-10-01T00:00:00Z
Publisher	Galenos Yayinevi
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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