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Article: SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants

Chung, Hoyin / Yeong Noh, Ji / Koo, Bon-Sang / Joo Hong, Jung / Kwon Kim, Hye

Computational and Structural Biotechnology Journal. 2022 Apr. 15,

2022

Abstract: Since the outbreak of coronavirus disease (COVID-19) in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into diverse variants. Here, an early isolate of SARS-CoV-2 was serially passaged in multiple cell lines of human ... ...

Abstract	Since the outbreak of coronavirus disease (COVID-19) in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into diverse variants. Here, an early isolate of SARS-CoV-2 was serially passaged in multiple cell lines of human origin in triplicate, and selected mutations were compared to those found in natural SARS-CoV-2 variants. In the spike protein, Q493R and Q498R substitutions from passaged viruses were consistent with those in the B.1.1.529 (Omicron) variant. Y144del and H655Y substitutions from passaged viruses were also reported in B.1.1.7 (Alpha), P.1 (Gamma), and B.1.1.529 (Omicron) variants. Several single nucleotide polymorphisms (SNPs) found in first-passaged viruses have also been identified as selected mutation sites in serially passaged viruses. Considering the consistent mutations found between serially passaged SARS-CoV-2 and natural variants, there may be host-specific selective mutation patterns of viral evolution in humans. Additional studies on the selective mutations in SARS-CoV-2 experiencing diverse host environments will help elucidate the direction of SARS-CoV-2 evolution. SARS-CoV-2 isolate (SARS-CoV-2/human/KOR/KCDC03-NCCP43326/2020) was serially passaged in A549, CaCO2, and HRT-18 cells in triplicate. After 12 times of serial passages in each cell lines, several consistent selected mutations were found on spike protein between the serially passaged SARS-CoV-2 in human cell lines and recent natural variants of SARS-CoV-2 like omicron. On the non-spike protein genes, selected mutations were more frequent in viruses passaged in Caco-2 and HRT-18 cells (Colon epithelial-like) than in those passaged in A549 cells (Lung epithelial-like). In addition, several SNPs identified after one round of passaging were consistently identified as the selected mutation sites in serially passaged viruses. Thus, mutation patterns of SARS-CoV-2 in certain host environments may provide researchers information to understand and predict future SARS-CoV-2 variants.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; biotechnology ; colon ; host specificity ; humans ; lungs ; mutation
Language	English
Dates of publication	2022-0415
Publishing place	Elsevier B.V.
Document type	Article
Note	Pre-press version
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.04.022
Database	NAL-Catalogue (AGRICOLA)

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Article: SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants.

Chung, Hoyin / Noh, Ji Yeong / Koo, Bon-Sang / Hong, Jung Joo / Kim, Hye Kwon

Computational and structural biotechnology journal

2022 Volume 20, Page(s) 1925–1934

Abstract	Since the outbreak of coronavirus disease (COVID-19) in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into diverse variants. Here, an early isolate of SARS-CoV-2 was serially passaged in multiple cell lines of human origin in triplicate, and selected mutations were compared to those found in natural SARS-CoV-2 variants. In the spike protein, Q493R and Q498R substitutions from passaged viruses were consistent with those in the B.1.1.529 (Omicron) variant. Y144del and H655Y substitutions from passaged viruses were also reported in B.1.1.7 (Alpha), P.1 (Gamma), and B.1.1.529 (Omicron) variants. Several single nucleotide polymorphisms (SNPs) found in first-passaged viruses have also been identified as selected mutation sites in serially passaged viruses. Considering the consistent mutations found between serially passaged SARS-CoV-2 and natural variants, there may be host-specific selective mutation patterns of viral evolution in humans. Additional studies on the selective mutations in SARS-CoV-2 experiencing diverse host environments will help elucidate the direction of SARS-CoV-2 evolution. Importance: SARS-CoV-2 isolate (SARS-CoV-2/human/KOR/KCDC03-NCCP43326/2020) was serially passaged in A549, CaCO2, and HRT-18 cells in triplicate. After 12 times of serial passages in each cell lines, several consistent selected mutations were found on spike protein between the serially passaged SARS-CoV-2 in human cell lines and recent natural variants of SARS-CoV-2 like omicron. On the non-spike protein genes, selected mutations were more frequent in viruses passaged in Caco-2 and HRT-18 cells (Colon epithelial-like) than in those passaged in A549 cells (Lung epithelial-like). In addition, several SNPs identified after one round of passaging were consistently identified as the selected mutation sites in serially passaged viruses. Thus, mutation patterns of SARS-CoV-2 in certain host environments may provide researchers information to understand and predict future SARS-CoV-2 variants.
Language	English
Publishing date	2022-04-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.04.022
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Article ; Online: The Blood Microbiome and Health

Hong Sheng Cheng / Sin Pei Tan / David Meng Kit Wong / Wei Ling Yolanda Koo / Sunny Hei Wong / Nguan Soon Tan

International Journal of Molecular Sciences, Vol 24, Iss 5633, p

Current Evidence, Controversies, and Challenges

2023 Volume 5633

Abstract: Blood is conventionally thought to be sterile. However, emerging evidence on the blood microbiome ... of microbes or pathogens in the blood circulation, leading to the conceptualization of a blood microbiome ... that is vital for physical wellbeing. Dysbiosis of the blood microbial profile has been implicated ...

Abstract	Blood is conventionally thought to be sterile. However, emerging evidence on the blood microbiome has started to challenge this notion. Recent reports have revealed the presence of genetic materials of microbes or pathogens in the blood circulation, leading to the conceptualization of a blood microbiome that is vital for physical wellbeing. Dysbiosis of the blood microbial profile has been implicated in a wide range of health conditions. Our review aims to consolidate recent findings about the blood microbiome in human health and to highlight the existing controversies, prospects, and challenges around this topic. Current evidence does not seem to support the presence of a core healthy blood microbiome. Common microbial taxa have been identified in some diseases, for instance, Legionella and Devosia in kidney impairment, Bacteroides in cirrhosis, Escherichia/Shigella and Staphylococcus in inflammatory diseases, and Janthinobacterium in mood disorders. While the presence of culturable blood microbes remains debatable, their genetic materials in the blood could potentially be exploited to improve precision medicine for cancers, pregnancy-related complications, and asthma by augmenting patient stratification. Key controversies in blood microbiome research are the susceptibility of low-biomass samples to exogenous contamination and undetermined microbial viability from NGS-based microbial profiling, however, ongoing initiatives are attempting to mitigate these issues. We also envisage future blood microbiome research to adopt more robust and standardized approaches, to delve into the origins of these multibiome genetic materials and to focus on host–microbe interactions through the elaboration of causative and mechanistic relationships with the aid of more accurate and powerful analytical tools.
Keywords	host–microbe interaction ; microbial commensalism ; dysbiosis ; bacterial translocation ; septicaemia ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Measurement of 3D Wrist Angles by Combining Textile Stretch Sensors and AI Algorithm.

Kim, Jae-Ha / Koo, Bon-Hak / Kim, Sang-Un / Kim, Joo-Yong

Sensors (Basel, Switzerland)

2024 Volume 24, Issue 5

Abstract: The wrist is one of the most complex joints in our body, composed of eight bones. Therefore, measuring the angles of this intricate wrist movement can prove valuable in various fields such as sports analysis and rehabilitation. Textile stretch sensors ... ...

Abstract	The wrist is one of the most complex joints in our body, composed of eight bones. Therefore, measuring the angles of this intricate wrist movement can prove valuable in various fields such as sports analysis and rehabilitation. Textile stretch sensors can be easily produced by immersing an E-band in a SWCNT solution. The lightweight, cost-effective, and reproducible nature of textile stretch sensors makes them well suited for practical applications in clothing. In this paper, wrist angles were measured by attaching textile stretch sensors to an arm sleeve. Three sensors were utilized to measure all three axes of the wrist. Additionally, sensor precision was heightened through the utilization of the Multi-Layer Perceptron (MLP) technique, a subtype of deep learning. Rather than fixing the measurement values of each sensor to specific axes, we created an algorithm utilizing the coupling between sensors, allowing the measurement of wrist angles in three dimensions. Using this algorithm, the error angle of wrist angles measured with textile stretch sensors could be measured at less than 4.5°. This demonstrated higher accuracy compared to other soft sensors available for measuring wrist angles.
Language	English
Publishing date	2024-03-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s24051685
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Article ; Online: Ischemia With Nonobstructive Coronary Artery Disease: Concept, Assessment, and Management.

Hwang, Doyeon / Park, Sang-Hyeon / Koo, Bon-Kwon

JACC. Asia

2023 Volume 3, Issue 2, Page(s) 169–184

Abstract: In daily clinical practice, physicians often encounter patients with angina or those with evidence of myocardial ischemia from noninvasive tests but not having obstructive coronary artery disease. This type of ischemic heart disease is referred to as ... ...

Abstract	In daily clinical practice, physicians often encounter patients with angina or those with evidence of myocardial ischemia from noninvasive tests but not having obstructive coronary artery disease. This type of ischemic heart disease is referred to as ischemia with nonobstructive coronary arteries (INOCA). INOCA patients often suffer from recurrent chest pain without adequate management and are associated with poor clinical outcomes. There are several endotypes of INOCA, and each endotype should be treated based on its specific underlying mechanism. Therefore, identifying INOCA and discriminating its underlying mechanisms are important issues and of clinical interest. Invasive physiologic assessment is the first step in the diagnosis of INOCA and discriminating the underlying mechanism; additional provocation tests help physicians identify the vasospastic component in INOCA patients. Comprehensive information acquired from these invasive tests can provide a template for mechanism-specific management for patients with INOCA.
Language	English
Publishing date	2023-04-18
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2772-3747
ISSN (online)	2772-3747
DOI	10.1016/j.jacasi.2023.01.004
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Article ; Online: Effect of Maxillary Sinus Pneumatization on the Ease of Access to Prelacrimal Recess.

Son, Sang-Jun / Koo, Hyung-Bon / Lee, Jae-Hoon

Ear, nose, & throat journal

2023 , Page(s) 1455613231174138

Abstract: Objective: Prelacrimal recess approach can be used to access lesions of the anterior wall of the maxillary sinus (MS). Moreover, the longer the prelacrimal recess window distance (PLRWD), the easier it is to access the anterior wall. This study aimed to ...

Abstract	Objective: Prelacrimal recess approach can be used to access lesions of the anterior wall of the maxillary sinus (MS). Moreover, the longer the prelacrimal recess window distance (PLRWD), the easier it is to access the anterior wall. This study aimed to define the correlation between maxillary sinus pneumatization (MSP) and PLRWD, a previously defined anatomic factor predictive of the ease of prelacrimal recess approach (PLRA). Methods: In total, 506 sides of 253 participants were studied. In the axial image, the PLRWD, the distance between the anterior wall of the MS and the lacrimal duct, was measured through radioanatomical analysis and classified as type I (<3 mm), type II (3-7 mm), or type III (>7 mm). On the coronal image, the distance between the nasal floor and the lower end of the MS was measured. When MSP did not reach the nasal floor, it was classified as grade I, as grade II when MSP reached the nasal floor, and grade III when the MS was pneumatized below the nasal floor. Results: Type I included 115 sides (22.7%); type II, 277 sides (54.7%); and type III, 114 sides (22.5%). Grade I was observed in 58 sides (11.5%), grade II in 38 sides (7.5%), and grade III in 410 sides (81.0%). The mean PLRWD of grade I was 2.35 ± 2.41 mm, II was 3.37 ± 2.46 mm, and III was 5.55 ± 2.54 mm, showing a significant difference ( Conclusions: This study demonstrates a correlation between the feasibility of MSP and PLRA. Both MSP and PLRWD are essential diagnostic parameters for preoperative planning and better surgical outcomes.
Language	English
Publishing date	2023-05-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	750153-5
ISSN	1942-7522 ; 0145-5613
ISSN (online)	1942-7522
ISSN	0145-5613
DOI	10.1177/01455613231174138
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Article ; Online: The Blood Microbiome and Health: Current Evidence, Controversies, and Challenges.

Cheng, Hong Sheng / Tan, Sin Pei / Wong, David Meng Kit / Koo, Wei Ling Yolanda / Wong, Sunny Hei / Tan, Nguan Soon

International journal of molecular sciences

2023 Volume 24, Issue 6

Abstract	Blood is conventionally thought to be sterile. However, emerging evidence on the blood microbiome has started to challenge this notion. Recent reports have revealed the presence of genetic materials of microbes or pathogens in the blood circulation, leading to the conceptualization of a blood microbiome that is vital for physical wellbeing. Dysbiosis of the blood microbial profile has been implicated in a wide range of health conditions. Our review aims to consolidate recent findings about the blood microbiome in human health and to highlight the existing controversies, prospects, and challenges around this topic. Current evidence does not seem to support the presence of a core healthy blood microbiome. Common microbial taxa have been identified in some diseases, for instance,
MeSH term(s)	Humans ; Microbiota ; Host Microbial Interactions ; Legionella ; Dysbiosis/microbiology ; Forecasting
Language	English
Publishing date	2023-03-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24065633
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Article ; Online: Impact of sensitization and ABO blood types on the opportunity of deceased-donor kidney transplantation with prolonged waiting time.

Lee, Jin Hyeog / Koo, Tai Yeon / Lee, Jung Eun / Oh, Kook Hwan / Kim, Beom Seok / Yang, Jaeseok

Scientific reports

2024 Volume 14, Issue 1, Page(s) 2635

Abstract: ... We investigated the impact of sensitization and ABO blood type (ABO) on DDKT opportunity using two Korean cohorts ... groups, respectively, and 61.1%, 11.6%, and 27.3% belonged to A or B, AB, and O blood types, respectively ...

Abstract	The waiting time to deceased-donor kidney transplantation (DDKT) is long in Asian countries. We investigated the impact of sensitization and ABO blood type (ABO) on DDKT opportunity using two Korean cohorts: a hospital cohort from two centers and a national database. The impact of panel reactive antibody (PRA) based on the maximal PRA% and ABO on DDKT accessibility was analyzed using a competing risks regression model. In the hospital cohort (n = 4722), 88.2%, 8.7%, and 3.1% of patients belonged to < 80%, 80-99%, and ≥ 99% PRA groups, respectively, and 61.1%, 11.6%, and 27.3% belonged to A or B, AB, and O blood types, respectively. When PRA and ABO were combined, PRA < 80%/A or B and 80 ≤ PRA < 99%/AB had fewer DDKT opportunities (median, 12 years; subdistribution hazard ratio [sHR], 0.71) compared with PRA < 80%/AB (median, 11 years). Also, PRA < 80%/O, 80 ≤ PRA < 99%/A or B, and PRA ≥ 99%/AB had a much lower DDKT opportunity (median, 13 years; sHR, 0.49). Furthermore, 80 ≤ PRA < 99%/O and PRA ≥ 99%/non-AB had the lowest DDKT opportunity (sHR, 0.28). We found similar results in the national cohort (n = 18,974). In conclusion, an integrated priority system for PRA and ABO is needed to reduce the inequity in DDKT opportunities, particularly in areas with prolonged waiting times.
MeSH term(s)	Humans ; Kidney Transplantation/methods ; Tissue Donors ; Waiting Lists ; Kidney ; Blood Grouping and Crossmatching
Language	English
Publishing date	2024-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-53157-2
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Article ; Online: Comparative spatial transcriptomic profiling of severe acute respiratory syndrome coronavirus 2 Delta and Omicron variants infections in the lungs of cynomolgus macaques.

Oh, Taehwan / Kim, Green / Baek, Seung Ho / Woo, YoungMin / Koo, Bon-Sang / Hwang, Eun-Ha / Shim, Kyuyoung / An, You Jung / Kim, Yujin / Park, Jae-Hak / Hong, Jung Joo

Journal of medical virology

2023 Volume 95, Issue 6, Page(s) e28847

Abstract: Recently emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants are generally less pathogenic than previous strains. However, elucidating the molecular basis for pulmonary immune response alterations is challenging owing ... ...

Abstract	Recently emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants are generally less pathogenic than previous strains. However, elucidating the molecular basis for pulmonary immune response alterations is challenging owing to the virus's heterogeneous distribution within complex tissue structure. Here, we revealed the spatial transcriptomic profiles of pulmonary microstructures at the SARS-CoV-2 infection site in the nine cynomolgus macaques upon inoculation with the Delta and Omicron variants. Delta- and Omicron-infected lungs had upregulation of genes involved in inflammation, cytokine response, complement, cell damage, proliferation, and differentiation pathways. Depending on the tissue microstructures (alveoli, bronchioles, and blood vessels), there were differences in the types of significantly upregulated genes in each pathway. Notably, a limited number of genes involved in cytokine and cell damage response were differentially expressed between bronchioles of the Delta- and Omicron-infection groups. These results indicated that despite a significant antigenic shift in SARS-CoV-2, the host immune response mechanisms induced by the variants were relatively consistent, with limited transcriptional alterations observed only in large airways. This study may aid in understanding the pathogenesis of SARS-CoV-2 and developing a clinical strategy for addressing immune dysregulation by identifying potential transcriptional biomarkers within pulmonary microstructures during infection with emerging variants.
MeSH term(s)	Animals ; SARS-CoV-2/genetics ; Transcriptome ; COVID-19/genetics ; Pulmonary Alveoli ; Cytokines/genetics ; Macaca
Chemical Substances	Cytokines
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28847
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Article ; Online: Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques.

Oh, Taehwan / Kim, Green / Baek, Seung Ho / Woo, YoungMin / Koo, Bon-Sang / Hwang, Eun-Ha / Shim, Kyuyoung / An, You Jung / Kim, Yujin / Won, Jinyoung / Lee, Youngjeon / Lim, Kyung Seob / Park, Jae-Hak / Hong, Jung Joo

Communications biology

2023 Volume 6, Issue 1, Page(s) 879

Abstract: Characterizing the host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the molecular level is necessary to understand viral pathogenesis and identify clinically relevant biomarkers. However, in humans, the pulmonary host ... ...

Abstract	Characterizing the host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the molecular level is necessary to understand viral pathogenesis and identify clinically relevant biomarkers. However, in humans, the pulmonary host response during disease onset remains poorly understood. Herein, we utilized a spatial transcriptome atlas to identify pulmonary microstructure-specific COVID-19 gene signatures during the acute phase of lung infection in cynomolgus macaques. The innate immune response to virus-induced cell death was primarily active in the alveolar regions involving activated macrophage infiltration. Inflamed vascular regions exhibited prominent upregulation of interferon and complement pathway genes that mediate antiviral activity and tissue damage response. Furthermore, known biomarker genes were significantly expressed in specific microstructures, and some of them were universally expressed across all microstructures. These findings underscore the importance of identifying key drivers of disease progression and clinically applicable biomarkers by focusing on pulmonary microstructures appearing during SARS-CoV-2 infection.
MeSH term(s)	Humans ; Animals ; COVID-19/genetics ; SARS-CoV-2 ; Transcriptome ; Ascomycota ; Macaca fascicularis ; Lung
Language	English
Publishing date	2023-08-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05253-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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