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Dirican E, Savrun ŞT, Aydın İE, Gülbay G, Karaman Ü. ANALYSIS OF MITOCHONDRIAL DNA CYTOCHROME-B ( CYB) and ATPase-6 GENE MUTATIONS IN COVID-19 PATIENTS. J Med Virol 2022; 94:3138-3146. [PMID: 35258110 PMCID: PMC9088694 DOI: 10.1002/jmv.27704] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Coronavirus disease of 2019 (COVID-19) is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Mutations of mitochondrial DNA (mtDNA) are becoming increasingly common in various diseases. This study aims to investigate mutations in the cytochrome-b (CYB) and adenosine triphosphatase-6 (ATPase-6) genes of mtDNA in COVID-19 patients. The association between mtDNA mutations and clinical outcomes is investigated. METHODS In the present study, mutations of the mtDNA genes CYB and ATPase-6 were investigated in COVID-19(+) (n=65) and COVID-19 (-) patients (n=65). First, we isolated DNA from the blood samples. After the PCR analyses, the mutations were defined using Sanger DNA sequencing. RESULTS The age, creatinine, ferritin and CRP levels of the COVID 19 (+) patients were higher than those of the COVID-19 (-) patients (p=0.0036, p=0.0383, p=0.0305, p<0.0001, respectively). We also found 16 different mutations in the CYB gene and 14 different mutations in the ATPase-6 gene. The incidences of CYB gene mutations A15326G, T15454C and C15452A were higher in COVID-19 (+) patients than COVID-19 (-) patients (p<0.0001 (OR (95% CI): 4.966 (2.215-10.89)), p=0.0226 and p=0.0226, respectively). In contrast, the incidences of A8860G and G9055A ATPase-6 gene mutations were higher in COVID-19 (+) patients than COVID-19 (-) patients (p<0.0001 (OR (95%CI): 5.333 (2.359-12.16) and p=0.0121 respectively). Yet, no significant relationship was found between mtDNA mutations and patients' age and biochemical parameters (p> 0.05). CONCLUSIONS The results showed that the frequency of mtDNA mutations in COVID-19 patients is quite high and it is important to investigate the association of these mutations with other genetic mechanisms in larger patient populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ebubekir Dirican
- Bayburt University, Health Services Vocational School, Bayburt, Turkey
| | - Şeyda Tuba Savrun
- Department of Emergency Medicine, Ordu University Faculty of Medicine, Ordu, Turkey
| | - İsmail Erkan Aydın
- Department of Emergency Medicine, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Gonca Gülbay
- Department of Medical Biology, Ordu University Faculty of Medicine, Ordu, Turkey
| | - Ülkü Karaman
- Department of Parasitology, Ordu University Faculty of Medicine, Ordu, Turkey
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Pasic L, Goterris L, Guerrero-Murillo M, Irinyi L, Kan A, Ponce CA, Vargas SL, Martin-Gomez MT, Meyer W. Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii. J Fungi (Basel) 2020; 6:E259. [PMID: 33143112 DOI: 10.3390/jof6040259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 12/26/2022] Open
Abstract
Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, β-TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: β-TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen.
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Barbhuiya PA, Uddin A, Chakraborty S. Analysis of compositional properties and codon usage bias of mitochondrial CYB gene in anura, urodela and gymnophiona. Gene 2020; 751:144762. [PMID: 32407767 DOI: 10.1016/j.gene.2020.144762] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023]
Abstract
We delineated the pattern of synonymous codon usage bias (CUB) and its determinants in mitochondrial CYB gene of respiratory chain across different amphibian groups namely orders anura, urodela and gymnophiona. We observed that CUB was low in CYB gene of amphibia. The gymnophionans had comparatively high bias followed by urodeles and anurans. The codons namely TCA, CCA, CAA, CGA, TGA, AAA and ACA were over-represented in all three orders. The codons such as GCC and TCC were over-represented in anura whereas in urodela, the over-represented codons were TTA, CTA, ATA, GTA, GAA, GGA and GCA. In gymnophiona, GCC, TTA, CTA, ATA, GTA, GAA and GGA codons were over-represented. The regression analysis between effective number of codons (ENC) and nucleobase at the 3rd position revealed that nucleobase A and C influenced CUB positively in order anura, while in urodela and gymnophiona, nucleobase A and T influenced the CUB positively. Mutation pressure and natural selection mutually illustrate the CUB of CYB gene (complex III gene) of amphibia as elucidated by correlation analysis between 3rd nucleotide in a codon and overall nucleotide content of the gene. However, neutrality plot showed that natural selection was the dominant evolutionary factor of CUB.
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Affiliation(s)
- Parvin A Barbhuiya
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakand 788150, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
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Sürgeç E, Can H, Döşkaya M, Karakavuk M, Atalay Şahar E, Değirmenci Döşkaya A, Pullukçu H, Taşbakan M, Sezai Taşbakan M, Akyol D, Yargucu Zihni F, Ün C, Yüksel Gürüz A, Demir S. Genotyping of Pneumocystis jirovecii isolates obtained from clinical samples by multilocus sequencing: a molecular epidemiology study conducted in Turkey. Arch Microbiol 2020; 202:1647-1652. [PMID: 32274557 DOI: 10.1007/s00203-020-01874-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/20/2020] [Accepted: 04/01/2020] [Indexed: 12/12/2022]
Abstract
Pneumocystis jirovecii is an opportunistic respiratory pathogen causing Pneumocystis pneumonia (PcP) in immunocompromised patients. The aim of this study was to investigate the genetic diversity of P. jirovecii isolates (n: 84) obtained from PcP patients using multilocus sequencing method based on mt26S, SOD, and CYB loci. Among the 84 clinical samples that were positive for P. jirovecii DNA, 31 (36.90%) of them were genotyped using at least one locus. Of the 31 clinical samples, 26 of them were successfully genotyped using all loci whereas three samples were genotyped using either mt26S/CYB loci or mt26S/SOD loci. Additionally, there were two more clinical samples that were genotyped using CYB or SOD locus. Using mt26S locus, genotypes 2, 3, 7, and 8 were detected. Frequencies of genotype 7 and 8 were higher and both of them were found in 11 (n: 29; 37.93%) clinical samples. Using SOD locus, SOD 1, 2, and 4 genotypes were detected. SOD 1 was the predominant genotype (20/28; 71.42%). During the analyses of CYB locus, CYB 1, 2, 5, 6, and 7 as well as a new CYB genotype were detected. CYB 1 (16/29; 55.17%) and 2 (10/29; 34.48%) were the predominant genotypes. Overall, according to the multilocus sequencing results E, F, M, N, P, and V multilocus genotypes were detected among the PcP patients. In addition, SOD 1 was the predominant genotype and CYB had a more polymorphic locus.
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Affiliation(s)
- Ecem Sürgeç
- Faculty of Science, Department of Biology, Zoology Section, Ege University, Izmir, Turkey
| | - Hüseyin Can
- Faculty of Science, Department of Biology, Molecular Biology Section, Ege University, Izmir, Turkey
| | - Mert Döşkaya
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, Turkey
| | | | - Esra Atalay Şahar
- Faculty of Engineering, Department of Biotechnology, Ege University, Izmir, Turkey
| | - Aysu Değirmenci Döşkaya
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, Turkey.,Faculty of Medicine, Blood Bank, Ege University, Izmir, Turkey
| | - Hüsnü Pullukçu
- Faculty of Medicine, Department of Infectious Diseases, Ege University, Izmir, Turkey
| | - Meltem Taşbakan
- Faculty of Medicine, Department of Infectious Diseases, Ege University, Izmir, Turkey
| | | | - Deniz Akyol
- Faculty of Medicine, Department of Infectious Diseases, Ege University, Izmir, Turkey
| | - Figen Yargucu Zihni
- Faculty of Medicine, Department of Rheumatology, Ege University, Izmir, Turkey
| | - Cemal Ün
- Faculty of Science, Department of Biology, Molecular Biology Section, Ege University, Izmir, Turkey
| | - Adnan Yüksel Gürüz
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, Turkey
| | - Samiye Demir
- Faculty of Science, Department of Biology, Zoology Section, Ege University, Izmir, Turkey.
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