|
1
|
Lim HJ, Lee JY, Baek YH, Park MY, Youm DJ, Kim I, Kim MJ, Choi J, Sohn YH, Park JE, Yang YJ. Evaluation of Multiplex Rapid Antigen Tests for the Simultaneous Detection of SARS-CoV-2 and Influenza A/B Viruses. Biomedicines 2023; 11:3267. [PMID: 38137488 PMCID: PMC10741453 DOI: 10.3390/biomedicines11123267] [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: 11/13/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Single-target rapid antigen tests (RATs) are commonly used to detect highly transmissible respiratory viruses (RVs), such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses. The simultaneous detection of RVs presenting overlapping symptoms is vital in making appropriate decisions about treatment, isolation, and resource utilization; however, few studies have evaluated multiplex RATs for SARS-CoV-2 and other RVs. We assessed the diagnostic performance of multiplex RATs targeting both the SARS-CoV-2 and influenza A/B viruses with the GenBody Influenza/COVID-19 Ag Triple, InstaView COVID-19/Flu Ag Combo (InstaView), STANDARDTM Q COVID-19 Ag Test, and STANDARDTM Q Influenza A/B Test kits using 974 nasopharyngeal swab samples. The cycle threshold values obtained from the real-time reverse transcription polymerase chain reaction results showed higher sensitivity (72.7-100%) when the values were below, rather than above, the cut-off values. The InstaView kit exhibited significantly higher positivity rates (80.21% for SARS-CoV-2, 61.75% for influenza A, and 46.15% for influenza B) and cut-off values (25.57 for SARS-CoV-2, 21.19 for influenza A, and 22.35 for influenza B) than the other two kits, and was able to detect SARS-CoV-2 Omicron subvariants. Therefore, the InstaView kit is the best choice for routine screening for both SARS-CoV-2 and influenza A/B in local communities.
Collapse
Affiliation(s)
- Ho-Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Republic of Korea
| | - Ji-Yoon Lee
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Young-Hyun Baek
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Min-Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Dong-Jae Youm
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Inhee Kim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Min-Jin Kim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Jongmun Choi
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Yong-Hak Sohn
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| | - Jung-Eun Park
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Republic of Korea
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (H.-J.L.); (J.-Y.L.); (Y.-H.B.); (M.-Y.P.); (D.-J.Y.); (I.K.); (M.-J.K.); (J.C.); (Y.-H.S.)
| |
Collapse
|
|
2
|
Baek YH, Park MY, Lim HJ, Youm DJ, You Y, Ahn S, Park JE, Kim MJ, Lee SH, Sohn YH, Yang YJ. Evaluation of Rapid Multiplex Reverse Transcription-Quantitative Polymerase Chain Reaction Assays for SARS-CoV-2 Detection in Individual and Pooled Samples. Life (Basel) 2023; 13:1717. [PMID: 37629574 PMCID: PMC10455980 DOI: 10.3390/life13081717] [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: 07/13/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Although coronavirus disease 2019 (COVID-19) is no longer a Public Health Emergency of International Concern (PHEIC), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has had a vast impact to date. Hence, continuous management is required, given the uncertainty caused by the potential evolution of SARS-CoV-2. Reverse transcription-quantitative PCR (RT-qPCR) diagnosis has been fundamental in overcoming this issue. In this study, the performances of two rapid RT-qPCR assays (Real-Q Direct SARS-CoV-2 Detection Kit and Allplex™ SARS-CoV-2 fast PCR Assay) with short PCR times were comparatively evaluated using a STANDARD M nCoV Real-Time Detection Kit (STANDARD M, conventional RT-qPCR assay). All kits showed a limit of detection values (102-103 copies/reaction). The evaluation showed that the two rapid assay tests had ≥97.89% sensitivity and ≥99.51% specificity (κ = 0.98) for individual samples and ≥97.32% sensitivity and ≥97.67% specificity for pooled samples compared to STANDARD M. These results indicate that the two rapid RT-qPCR kits, which showed significant time reduction in performance, are as effective as a conventional RT-qPCR assay. They are likely to increase not only the number of tests that can be performed but also the efficiency of sustainable management of COVID-19 in the long term.
Collapse
Affiliation(s)
- Young-Hyun Baek
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Min-Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Ho-Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Republic of Korea;
| | - Dong-Jae Youm
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Youngshin You
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Seojin Ahn
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Jung-Eun Park
- Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Republic of Korea;
| | - Min-Jin Kim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Sun-Hwa Lee
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul 04805, Republic of Korea;
| | - Yong-Hak Sohn
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul 04805, Republic of Korea; (Y.-H.B.); (M.-Y.P.); (H.-J.L.); (D.-J.Y.); (Y.Y.); (S.A.); (M.-J.K.); (Y.-H.S.)
| |
Collapse
|
|
3
|
Youm DJ, Ko BJ, Kim D, Park M, Won S, Lee YH, Kim B, Seol D, Chai HH, Lim D, Jeong C, Kim H. The idiosyncratic genome of Korean long-tailed chicken as a valuable genetic resource. iScience 2023; 26:106236. [PMID: 36915682 PMCID: PMC10006692 DOI: 10.1016/j.isci.2023.106236] [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: 11/03/2022] [Revised: 11/28/2022] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
Today, breeds with ornamental traits such as exceptionally long tail feathers are economically valuable. However, the genetic basis of long-tail feathers is yet to be understood. To provide better understanding of long tail feathers, we sequenced Korean long-tailed chicken (KLC) genomes and compared them with genomes of other chicken breeds. We first analyzed the genome structure of KLC and its genomic relationship with other chickens and observed unique characteristics. Subsequently, we searched for genomic regions under selection. Feather keratin 1-like enriched region and several genes were found to have novel putative functions and effects on the long tail trait in KLC. Our findings support the value of KLC as a unique genetic resource and cast light on the genetic basis of long tail traits in avian species. We expect this novel knowledge to provide new genomic evidence and options for designing and implementing genetic improvements of ornamental chicken productivity through precision crossbreeding aids.
Collapse
Affiliation(s)
- Dong-Jae Youm
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Donghee Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sohyoung Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
- eGnome, Inc, Seoul 05836, Republic of Korea
| | - Young Ho Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- eGnome, Inc, Seoul 05836, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA 1500, Wanju 55365, Republic of Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA 1500, Wanju 55365, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Corresponding author
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
- eGnome, Inc, Seoul 05836, Republic of Korea
- Corresponding author
| |
Collapse
|
|
4
|
Charton C, Youm DJ, Ko BJ, Seol D, Kim B, Chai HH, Lim D, Kim H. The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken). BMC Genomics 2021; 22:594. [PMID: 34348642 PMCID: PMC8340483 DOI: 10.1186/s12864-021-07903-9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. RESULTS The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. CONCLUSIONS Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.
Collapse
Affiliation(s)
- Clémentine Charton
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong-Jae Youm
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
| |
Collapse
|