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Article: Climate change and future infectious diseases: A growing threat.

Arikan, Ayse / Cakir, Nedim

2023 Volume 52, Page(s) 101088

Language	English
Publishing date	2023-01-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2750179-6
ISSN	2052-2975
ISSN	2052-2975
DOI	10.1016/j.nmni.2023.101088
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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: In Silico Evaluation of SARS-CoV-2 K417N, L452R, and E484K Detection Assays Against Omicron Variants.

Sayan, Murat / Arikan, Ayse / Isbilen, Murat

The new microbiologica

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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Zs.B 2267: Show issues

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Article ; Online: Quality of life after acute kidney injury.

McNicholas, Bairbre / Akcan Arikan, Ayse / Ostermann, Marlies

Current opinion in critical care

2023 Volume 29, Issue 6, Page(s) 566–579

Abstract: Purpose of review: Deciphering the effect of acute kidney injury (AKI) during critical illness on long-term quality of life versus the impact of conditions that brought on critical illness is difficult.: Recent findings: Reports on patient-centred ... ...

Abstract	Purpose of review: Deciphering the effect of acute kidney injury (AKI) during critical illness on long-term quality of life versus the impact of conditions that brought on critical illness is difficult. Recent findings: Reports on patient-centred outcomes such as health-related quality of life (HRQOL) have provided insight into the long-lasting impact of critical illness complicated by AKI. However, these data stem from observational studies and randomized controlled trials, which have been heterogeneous in their patient population, timing, instruments used for assessment and reporting. Recent studies have corroborated these findings including lack of effect of renal replacement therapy compared to severe AKI on outcomes and worse physical compared to cognitive dysfunction. Summary: In adults, more deficits in physical than mental health domains are found in survivors of AKI in critical care, whereas memory deficits and learning impairments have been noted in children. Further study is needed to understand and develop interventions that preserve or enhance the quality of life for individual patients who survive AKI following critical illness, across all ages.
MeSH term(s)	Adult ; Child ; Humans ; Quality of Life/psychology ; Critical Illness ; Acute Kidney Injury/therapy ; Acute Kidney Injury/complications ; Renal Replacement Therapy ; Critical Care
Language	English
Publishing date	2023-09-21
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	1235629-3
ISSN	1531-7072 ; 1070-5295
ISSN (online)	1531-7072
ISSN	1070-5295
DOI	10.1097/MCC.0000000000001090
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Zs.A 4999: Show issues

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Article ; Online: Current practices in pediatric continuous kidney replacement therapy: a systematic review-guided multinational modified Delphi consensus study.

Fuhrman, Dana Y / Gist, Katja M / Akcan-Arikan, Ayse

Pediatric nephrology (Berlin, Germany)

2023 Volume 38, Issue 8, Page(s) 2817–2826

Abstract: Background: Continuous kidney replacement therapy (CKRT) has become an integral part of the care of critically ill children. However, uncertainty exists regarding the current state of how CKRT is prescribed and delivered in children. The main objective ... ...

Abstract	Background: Continuous kidney replacement therapy (CKRT) has become an integral part of the care of critically ill children. However, uncertainty exists regarding the current state of how CKRT is prescribed and delivered in children. The main objective of this study was to identify the current practices for pediatric CKRT. Methods: We conducted a systematic review of the literature from 2012 to 2022 to identify data regarding CKRT timing of initiation, dosing, anticoagulation, fluid removal, and quality monitoring. Using this data, we then performed a two-round modified Delphi process using a multinational internet-assisted survey of prescribers of CKRT. Results: The survey was constructed using 172 articles that met inclusion criteria (12% of studies were pediatric focused). A total of 147 and 126 practitioners completed the survey in rounds 1 and 2, respectively. Participants represented Europe (9.5-11.6%) and North America including pediatric intensivists, nephrologists, and advance practice providers. Consensus (defined as a ≥ 75% participant response of "sometimes" or "always") was achieved for 26 statements. There was consensus in the practices of CKRT initiation, dosing, method of anticoagulation, and fluid removal. In contrast, there appears to be greater variability in the methods used for monitoring anticoagulation and the quality of the delivered treatment. Conclusions: Our study results suggest that the current state of pediatric CKRT practice is reflective of the literature over the last 10 years, which is largely based on the care of adult patients. This data provides a framework to study best practices to further improve outcomes for children receiving CKRT. A higher resolution version of the Graphical abstract is available as Supplementary information.
MeSH term(s)	Adult ; Child ; Humans ; Delphi Technique ; Acute Kidney Injury/therapy ; Continuous Renal Replacement Therapy/methods ; Blood Coagulation ; Anticoagulants/therapeutic use
Chemical Substances	Anticoagulants
Language	English
Publishing date	2023-01-10
Publishing country	Germany
Document type	Systematic Review ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-022-05864-z
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Zs.A 2196: Show issues

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Article ; Online: Trajectory of AKI in hospitalized pediatric patients-impact of duration and repeat events.

Moffett, Brady S / Arikan, Ayse Akcan

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association

2021 Volume 37, Issue 8, Page(s) 1443–1450

Abstract: Background: Peak severity of acute kidney injury (AKI) is associated with mortality in hospitalized pediatric patients. Other factors associated with AKI, such as number of AKI events, severity of AKI events and time spent in AKI, may also have ... ...

Abstract	Background: Peak severity of acute kidney injury (AKI) is associated with mortality in hospitalized pediatric patients. Other factors associated with AKI, such as number of AKI events, severity of AKI events and time spent in AKI, may also have associations with mortality. Characterization of these events could help to evaluate patient outcomes. Methods: Pediatric inpatients (<19 years of age) from 2011 to 2019 who were not on maintenance renal replacement therapy and had least one serum creatinine (SCr) obtained during hospital admission were included. Percent change in SCr from the minimum value in the prior 7 days was used for AKI staging according to Kidney Disease: Improving Global Outcomes (KDIGO) criteria. Maximum value for age appropriate normal was used for patients with only one SCr. Repeat AKI events were classified in patients if KDIGO criteria were met more than once with at least one SCr value between episodes that did not meet KDIGO criteria. Patient demographics were summarized and incidence of AKI was determined along with associations with mortality. AKI characterizations for the admission were developed including: AKI, repeat (more than one) AKI, AKI severity (maximum KDIGO stage) and total number of AKI events. AKI duration as percent admission days in a KDIGO stage and AKI percent velocity were determined. Kaplan-Meier analysis was performed for time to 30-day survival by AKI characterization. A mixed-effects logistic regression model with mortality as the dependent variable nested in patients was developed incorporating patient variables and AKI characterizations. Results: A total of 184 297 inpatient encounters met study criteria [male 51.7%, age 7.8 years (interquartile range 2.5-13.8) and mortality 0.56%]. Hospital length of stay was 1.9 days (IQR 0.37, 4.8 days), 15.4% had an intensive care unit admission and 12.2% underwent mechanical ventilation. AKI occurred in 5.6% (n = 10 246) of admissions [Stage 1, 4.5% (n = 8310); Stage 2, 1.3% (n = 2363); Stage 3, 0.77% (n = 1423)] and repeat AKI events occurred in 1.92% (n = 3558). AKI was associated with mortality (odds ratio 6.0, 95% confidence interval 4.8-7.6; P < 0.001) and increasing severity (KDIGO maximum stage) was associated with increased mortality. Multiple AKI events were also associated with mortality (P < 0.001). Duration of AKI was associated with mortality (P < 0.001) but AKI velocity was not (P > 0.05). Conclusions: AKI occurs in 5.6% of the pediatric inpatient population and multiple AKI events occur in ∼30% of these patients. Maximum KDIGO stage is most strongly associated with mortality. Multiple AKI events and AKI duration should also be considered when evaluating patient outcomes.
MeSH term(s)	Acute Kidney Injury/epidemiology ; Acute Kidney Injury/etiology ; Acute Kidney Injury/therapy ; Child ; Hospital Mortality ; Humans ; Male ; Renal Replacement Therapy/adverse effects ; Retrospective Studies ; Risk Factors
Language	English
Publishing date	2021-07-09
Publishing country	England
Document type	Journal Article
ZDB-ID	90594-x
ISSN	1460-2385 ; 0931-0509
ISSN (online)	1460-2385
ISSN	0931-0509
DOI	10.1093/ndt/gfab219
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Zs.A 2198: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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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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Zs.A 1928: Show issues

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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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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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