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Ibrahim F, Natasha A, Yasmon A, Rizal CT, Fithriyah, Karuniawati A, Saharman YR, Sudarmono P. Evaluation of SARS-CoV-2 quantification from oropharyngeal swabs, nasopharyngeal swabs, and naso-oropharyngeal swabs: A cross-sectional study. Heliyon 2024; 10:e28647. [PMID: 38586376 PMCID: PMC10998208 DOI: 10.1016/j.heliyon.2024.e28647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/02/2022] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
The current naso-oropharyngeal swab for SARS-CoV-2 detection faces several problems, such as waste issues and its use for quantitative studies. This study aimed to evaluate the total RNA and viral loads from different upper respiratory tract swabs types and whether SARS-CoV-2 quantification can use the current internal control for normalization. This cross-sectional study collected positive specimens with single oropharyngeal or nasopharyngeal swabs and naso-oropharyngeal swabs. The samples were extracted, tested with qualitative RT‒PCR, and then tested with quantitative RT‒PCR. The RNA eluate was measured for the total RNA concentration. The total RNA concentration, viral load, and RNaseP Ct values were collected and analysed statistically. The positive results came from 41 oropharyngeal swabs, 34 nasopharyngeal swabs, and 36 naso-oropharyngeal swabs. The total RNA increased significantly from oropharyngeal swabs to nasopharyngeal swabs to naso-oropharyngeal swabs. Significant differences in RNaseP Ct values between groups and their correlations with total RNA were found. In addition, the increase in the total RNA and the RNaseP Ct values were unrelated to the viral load. The physical features in the naso-oropharyngeal area and the swabbing procedures could affect the total RNA but not the viral load. However, since the virus particles could present inside and outside human cells, the increase in collected human cells may not always be followed by the viral load increase. Normalization using the RNaseP Ct value became unnecessary due to the factors mentioned above. Therefore, a careful approach is needed in viral load studies of swab specimens.
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Affiliation(s)
- Fera Ibrahim
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Augustine Natasha
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon 24252, Republic of Korea
| | - Andi Yasmon
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Chairunnisa Tawadhu Rizal
- Jakarta Health Laboratory Center, Ministry of Health, Percetakan Negara No.23B street, Central Jakarta, Indonesia
| | - Fithriyah
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Anis Karuniawati
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Yulia Rosa Saharman
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
| | - Pratiwi Sudarmono
- Department of Microbiology Faculty of Medicine Universitas Indonesia / Dr. Cipto Mangunkusumo Hospital, Pegangsaan Timur 16 Street, East Jakarta, 10430, Indonesia
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Lim T, Rajoriya S, Kim B, Natasha A, Im H, Shim HS, Yoo J, Kim JW, Lee EW, Shin HJ, Kim SH, Kim WK. In vitro broad-spectrum antiviral activity of MIT-001, a mitochondria-targeted reactive oxygen species scavenger, against severe acute respiratory syndrome coronavirus 2 and multiple zoonotic viruses. Virus Res 2024; 342:199325. [PMID: 38309472 PMCID: PMC10851010 DOI: 10.1016/j.virusres.2024.199325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/31/2023] [Accepted: 01/17/2024] [Indexed: 02/05/2024]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 becomes a serious threat to global health and requires the development of effective antiviral therapies. Current therapies that target viral proteins have limited efficacy with side effects. In this study, we investigated the antiviral activity of MIT-001, a small molecule reactive oxygen species (ROS) scavenger targeting mitochondria, against SARS-CoV-2 and other zoonotic viruses in vitro. The antiviral activity of MIT-001 was quantified by RT-qPCR and plaque assay. We also evaluated the functional analysis of MIT-001 by JC-1 staining to measure mitochondrial depolarization, total RNA sequencing to investigate gene expression changes, and immunoblot to quantify protein expression levels. The results showed that MIT-001 effectively inhibited the replication of B.1.617.2 and BA.1 strains, Zika virus, Seoul virus, and Vaccinia virus. Treatment with MIT-001 restored the expression of heme oxygenase-1 (HMOX1) and NAD(P)H: quinone oxidoreductase 1 (NqO1) genes, anti-oxidant enzymes reduced by SARS-CoV-2, to normal levels. The presence of MIT-001 also alleviated mitochondrial depolarization caused by SARS-CoV-2 infection. These findings highlight the potential of MIT-001 as a broad-spectrum antiviral compound that targets for zoonotic RNA and DNA viruses, providing a promising therapeutic approach to combat viral infection.
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Affiliation(s)
- Taehun Lim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Shivani Rajoriya
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Bohyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Augustine Natasha
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Hyeonjoo Im
- Laboratory of Regenerative Medicine For Neurodegenerative Disease, Stand Up Therapeutics, Hannamdaero 98, Seoul 04418, Republic of Korea
| | - Hyun Soo Shim
- Laboratory of Regenerative Medicine For Neurodegenerative Disease, Stand Up Therapeutics, Hannamdaero 98, Seoul 04418, Republic of Korea
| | - Junsang Yoo
- Laboratory of Regenerative Medicine For Neurodegenerative Disease, Stand Up Therapeutics, Hannamdaero 98, Seoul 04418, Republic of Korea
| | - Jong Woo Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34141, Republic of Korea; School of pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hye Jin Shin
- College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Soon Ha Kim
- Mitoimmune Therapeutics Inc., Gangnam-gu, Seoul 06253, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea; Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea.
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Prayitno SP, Natasha A, Lee S, Kim CM, Lee YM, Park K, Kim J, Kim SG, Park J, Rajoriya S, Palacios G, Oh Y, Song JW, Kim DM, Kim WK. Etiological agent and clinical characteristics of haemorrhagic fever with renal syndrome in the southern Republic of Korea: a genomic surveillance study. Clin Microbiol Infect 2024:S1198-743X(24)00089-2. [PMID: 38402954 DOI: 10.1016/j.cmi.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/23/2023] [Revised: 01/29/2024] [Accepted: 02/17/2024] [Indexed: 02/27/2024]
Abstract
OBJECTIVES High incidences of haemorrhagic fever with renal syndrome (HFRS) have been reported in the southern Republic of Korea (ROK). A distinct southern genotype of Orthohantavirus hantanense (HTNV) was identified in Apodemus agrarius chejuensis on Jeju Island. However, its association with HFRS cases in southern ROK remains elusive. We investigated the potential of the southern HTNV genotype as an etiological agent of HFRS. METHODS Samples from 22 patients with HFRS and 193 small mammals were collected in the southern ROK. The clinical characteristics of patients infected with the southern HTNV genotype were analysed. Amplicon-based MinION sequencing was employed for southern HTNV from patients and rodents, facilitating subsequent analyses involving phylogenetics and genetic reassortment. RESULTS High-throughput sequencing of HTNV exhibited higher coverage with a cycle of threshold value below 32, acquiring nearly whole-genome sequences from six patients with HFRS and seven A. agrarius samples. The phylogenetic pattern of patient-derived HTNV demonstrated genetic clustering with HTNV from Apodemus species on Jeju Island and the southern Korean peninsula, revealing genetic reassortment in a single clinical sample between the M and S segments. DISCUSSION These findings imply that the southern HTNV genotype has the potential to induce HFRS in humans. The phylogenetic inference demonstrates the diverse and dynamic characteristics of the southern HTNV tripartite genomes. Therefore, this study highlights the significance of active surveillance and amplicon sequencing for detecting orthohantavirus infections. It also raises awareness and caution for physicians regarding the emergence of a southern HTNV genotype as a cause of HFRS in the ROK.
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Affiliation(s)
- Sara P Prayitno
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Augustine Natasha
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Seonghyeon Lee
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Choon-Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - You Mi Lee
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Kyungmin Park
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea; BK21 Graduate Program, Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jongwoo Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea; BK21 Graduate Program, Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seong-Gyu Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea; BK21 Graduate Program, Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jieun Park
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Shivani Rajoriya
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yeonsu Oh
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea; BK21 Graduate Program, Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Dong-Min Kim
- Department of Internal Medicine, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea; Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea.
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Ibrahim F, Natasha A, Saharman YR, Yasmon A, Fithriyah F, Karuniawati A, Ganiesa S, Sudarmono P. Consideration of the Cycle Threshold Values from Real-Time RT-PCR SARS-CoV-2 Interpretation for the Clinicians: Analysis of 339 Positive Cases from a Referral Laboratory in Jakarta, Indonesia. Acta Med Indones 2021; 53:13-17. [PMID: 33818402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
BACKGROUND real-time RT-PCR was recommended by WHO for COVID-19 diagnosis. The cycle threshold (Ct) values were expected to have an association with clinical manifestation. However, the diagnostic modalities such as quantitative molecular detection and virus isolation were not yet available for the routine test. This study has been conducted to analyze the relationship between the Ct values of qualitative rRT-PCR and the clinical manifestation and to describe the factors determining the result. METHODS from March to April 2020, specimens were sent to our laboratory from different healthcare centers in Jakarta. The patient's characteristic and clinical manifestation were extracted from the specimen's epidemiology forms. The specimens extracted and tested using rRT-PCR, and the Ct value were collected. The data were analyzed using the appropriate statistic test. RESULTS from 339 positive results, the mild to moderate case was 176 (52%) and the severe cases was 163 (48%). Female was dominant in the mild to moderate cases (58%), while the male was prevalent in the severe cases (60%). The median age for mild to moderate case was 35 years old and severe cases was 49 years old. Statistical analysis found relationship between both group with gender (p = 0.001) and age (p < 0.001), but not with the Ct value. CONCLUSION many variables in specimen sampling and processing could affect the Ct value result. In addition, the disease's severity was depended with the host immune response, regardless the number of virus. There was suggested no significant difference between the Ct values of mild-moderate and severe COVID-19, and thus should not be loosely interpreted.
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Affiliation(s)
- Fera Ibrahim
- Clinical Microbiology Department, faculty of medicine, University of Indonesia.
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Ibrahim F, Natasha A, Saharman YR, Sudarmono P. Preliminary report of COVID-19 testing: experience of the clinical microbiology laboratory Universitas Indonesia, Jakarta, Indonesia. New Microbes New Infect 2020; 37:100733. [PMID: 32793354 PMCID: PMC7408335 DOI: 10.1016/j.nmni.2020.100733] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 12/25/2022] Open
Abstract
Indonesia first reported SARS-CoV-2 in March 2020. From March to April, clinical microbiology laboratory Universitas Indonesia in Jakarta received 4617 specimens with 12.6% positivity rate and 22% asymptomatic case. The result of this study could give an early picture of Indonesia’s COVID 19 outbreak situation.
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Affiliation(s)
- F Ibrahim
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/ Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - A Natasha
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/ Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Y R Saharman
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/ Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - P Sudarmono
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Indonesia/ Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
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Natasha A, Kafetz K. Use of the Geriatric Depression Score(GDS) to Predict Persistent Depressive Symptoms in Acute Elderly Medical Admissions. Age Ageing 1998. [DOI: 10.1093/ageing/27.suppl_2.39-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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