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Article ; Online: Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong.

Gu, Haogao / Chu, Daniel K W / Chang, Lydia D J / Cheuk, Sammi S Y / Gurung, Shreya / Krishnan, Pavithra / Ng, Daisy Y M / Liu, Gigi Y Z / Wan, Carrie K C / Xie, Ruopeng / Cheng, Samuel S M / Cowling, Benjamin J / Tsang, Dominic N C / Peiris, Malik / Dhanasekaran, Vijaykrishna / Poon, Leo L M

Emerging infectious diseases

2021 Volume 27, Issue 10, Page(s) 2666–2668

Abstract: We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our ... ...

Abstract	We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.
MeSH term(s)	COVID-19 ; Communicable Diseases, Imported ; Genetic Variation ; Hong Kong/epidemiology ; Humans ; SARS-CoV-2
Language	English
Publishing date	2021-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2710.211028
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Article ; Online: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia.

Chu, Daniel K W / Pan, Yang / Cheng, Samuel M S / Hui, Kenrie P Y / Krishnan, Pavithra / Liu, Yingzhi / Ng, Daisy Y M / Wan, Carrie K C / Yang, Peng / Wang, Quanyi / Peiris, Malik / Poon, Leo L M

Clinical chemistry

2020 Volume 66, Issue 4, Page(s) 549–555

Abstract: Background: A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially ... ...

Abstract	Background: A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially detected in Wuhan, a major city of China, but has subsequently been detected in other provinces of China. Travel-associated cases have also been reported in a few other countries. Outbreaks in health care workers indicate human-to-human transmission. Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients. Methods: We developed two 1-step quantitative real-time reverse-transcription PCR assays to detect two different regions (ORF1b and N) of the viral genome. The primer and probe sets were designed to react with this novel coronavirus and its closely related viruses, such as SARS coronavirus. These assays were evaluated using a panel of positive and negative controls. In addition, respiratory specimens from two 2019-nCoV-infected patients were tested. Results: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10-4-2000 TCID50/reaction). Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays. Samples from two 2019-nCoV-infected patients were positive in the tests. Conclusions: The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients.
MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/virology ; Disease Outbreaks ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/virology ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-02-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1093/clinchem/hvaa029
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Article ; Online: Measures of Patient Dissatisfaction With Health Care in Polycystic Ovary Syndrome: Retrospective Analysis.

Hoyos, Luis R / Putra, Manesha / Armstrong, Abigail A / Cheng, Connie Y / Riestenberg, Carrie K / Schooler, Tery A / Dumesic, Daniel A

Journal of medical Internet research

2020 Volume 22, Issue 4, Page(s) e16541

Abstract: Background: Polycystic ovary syndrome (PCOS) is a common reproductive and metabolic disorder in women; however, many clinicians may not be well versed in scientific advances that aid understanding of the associated reproductive, metabolic, and ... ...

Abstract	Background: Polycystic ovary syndrome (PCOS) is a common reproductive and metabolic disorder in women; however, many clinicians may not be well versed in scientific advances that aid understanding of the associated reproductive, metabolic, and psychological abnormalities. Women with PCOS are dissatisfied with health care providers, the diagnostic process, and the initial treatment of PCOS and seek information through alternative sources. This has affected the patient-physician relationship by allowing medical information acquired through the internet, whether correct or not, to become accessible to patients and reshape their health care perspective. Patient dissatisfaction with health care providers regarding PCOS raises questions about the responsibilities of academic institutions to adequately train and maintain the competence of clinicians and government agencies to sufficiently support scientific investigation in this field. Objective: The primary aim was to examine internet searching behaviors of the public regarding PCOS vs another highly prevalent gynecologic disorder. The secondary aim was to explore satisfaction with health care among patients with PCOS and their internet use. The tertiary aim was to examine medical education in reproductive endocrinology and infertility (REI) during obstetrics and gynecology (Ob/Gyn) residency as a proxy for physician knowledge in this field. Methods: Google search trends and StoryBase quantified monthly Google absolute search volumes for search terms related to PCOS and fibroids (January 2004 to December 2017; United States). The reproductive disorder, fibroids, was selected as a comparison group because of its high prevalence among women. Between female groups, monthly absolute search volumes and their trends were compared. A Web-based questionnaire (June 2015 to March 2018) explored health care experiences and the internet use of women with PCOS. REI rotation information during Ob/Gyn residency in the United States was obtained from the Association of Professors of Gynecology and Obstetrics website. Results: For PCOS (R=0.89; P<.01), but not fibroids (R=0.09; P=.25), monthly absolute search volumes increased significantly. PCOS-related monthly absolute search volumes (mean 384,423 searches, SD 88,756) were significantly greater than fibroid-related monthly absolute search volumes (mean 348,502 searches, SD 37,317; P<.05). PCOS was diagnosed by an Ob/Gyn in 60.9% (462/759) of patients, and 57.3% (435/759) of patients were dissatisfied with overall care. Among patients with PCOS, 98.2% (716/729) searched for PCOS on the Web but only 18.8% (143/729) of patients joined an online PCOS support group or forum. On average, Ob/Gyn residencies dedicated only 4% (2/43) of total block time to REI, whereas 5.5% (11/200) of such residencies did not offer any REI rotations. Conclusions: Over time, PCOS has been increasingly searched on the Web compared with another highly prevalent gynecologic disorder. Patients with PCOS are dissatisfied with their health care providers, who would benefit from an improved understanding of PCOS during Ob/Gyn residency training.
MeSH term(s)	Adolescent ; Adult ; Delivery of Health Care ; Female ; Humans ; Middle Aged ; Patient Satisfaction/statistics & numerical data ; Polycystic Ovary Syndrome/therapy ; Retrospective Studies ; Surveys and Questionnaires ; Young Adult
Language	English
Publishing date	2020-04-21
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2028830-X
ISSN	1438-8871 ; 1439-4456
ISSN (online)	1438-8871
ISSN	1439-4456
DOI	10.2196/16541
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Article ; Online: Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 10

Abstract: Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that ... ...

Abstract	Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that increased transmission followed prolonged periods of restrictions, likely due to adherence fatigue.
Keywords	Science ; Q
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong.

Nature communications

2022 Volume 13, Issue 1, Page(s) 736

Abstract: Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23- ... ...

Abstract	Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare.
MeSH term(s)	COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Genomics ; Hong Kong/epidemiology ; Humans ; Public Health ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Travel
Language	English
Publishing date	2022-02-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28420-7
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Article ; Online: The chromatin landscape of healthy and injured cell types in the human kidney.

Gisch, Debora L / Brennan, Michelle / Lake, Blue B / Basta, Jeannine / Keller, Mark S / Melo Ferreira, Ricardo / Akilesh, Shreeram / Ghag, Reetika / Lu, Charles / Cheng, Ying-Hua / Collins, Kimberly S / Parikh, Samir V / Rovin, Brad H / Robbins, Lynn / Stout, Lisa / Conklin, Kimberly Y / Diep, Dinh / Zhang, Bo / Knoten, Amanda /

Barwinska, Daria / Asghari, Mahla / Sabo, Angela R / Ferkowicz, Michael J / Sutton, Timothy A / Kelly, Katherine J / De Boer, Ian H / Rosas, Sylvia E / Kiryluk, Krzysztof / Hodgin, Jeffrey B / Alakwaa, Fadhl / Winfree, Seth / Jefferson, Nichole / Türkmen, Aydın / Gaut, Joseph P / Gehlenborg, Nils / Phillips, Carrie L / El-Achkar, Tarek M / Dagher, Pierre C / Hato, Takashi / Zhang, Kun / Himmelfarb, Jonathan / Kretzler, Matthias / Mollah, Shamim / Jain, Sanjay / Rauchman, Michael / Eadon, Michael T

Nature communications

2024 Volume 15, Issue 1, Page(s) 433

Abstract: There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive ... ...

Abstract	There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
MeSH term(s)	Humans ; Chromatin/genetics ; Kidney ; Kidney Tubules, Proximal ; Health Status ; Cell Count
Chemical Substances	Chromatin
Language	English
Publishing date	2024-01-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-44467-6
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Article ; Online: Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong

Haogao Gu / Daniel K.W. Chu / Lydia D.J. Chang / Sammi S.Y. Cheuk / Shreya Gurung / Pavithra Krishnan / Daisy Y.M. Ng / Gigi Y.Z. Liu / Carrie K.C. Wan / Ruopeng Xie / Samuel S.M. Cheng / Benjamin J. Cowling / Dominic N.C. Tsang / Malik Peiris / Vijaykrishna Dhanasekaran / Leo L.M. Poon

Emerging Infectious Diseases, Vol 27, Iss 10, Pp 2666-

2021 Volume 2668

Abstract	We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.
Keywords	coronavirus disease ; COVID-19 ; disease transmission control ; genomic diversity ; public health ; public health readiness ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The chromatin landscape of healthy and injured cell types in the human kidney

Debora L. Gisch / Michelle Brennan / Blue B. Lake / Jeannine Basta / Mark S. Keller / Ricardo Melo Ferreira / Shreeram Akilesh / Reetika Ghag / Charles Lu / Ying-Hua Cheng / Kimberly S. Collins / Samir V. Parikh / Brad H. Rovin / Lynn Robbins / Lisa Stout / Kimberly Y. Conklin / Dinh Diep / Bo Zhang / Amanda Knoten /

Daria Barwinska / Mahla Asghari / Angela R. Sabo / Michael J. Ferkowicz / Timothy A. Sutton / Katherine J. Kelly / Ian H. De Boer / Sylvia E. Rosas / Krzysztof Kiryluk / Jeffrey B. Hodgin / Fadhl Alakwaa / Seth Winfree / Nichole Jefferson / Aydın Türkmen / Joseph P. Gaut / Nils Gehlenborg / Carrie L. Phillips / Tarek M. El-Achkar / Pierre C. Dagher / Takashi Hato / Kun Zhang / Jonathan Himmelfarb / Matthias Kretzler / Shamim Mollah / the Kidney Precision Medicine Project (KPMP) / Sanjay Jain / Michael Rauchman / Michael T. Eadon

Nature Communications, Vol 15, Iss 1, Pp 1-

2024 Volume 21

Abstract: Abstract There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. ... ...

Abstract	Abstract There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney’s active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
Keywords	Science ; Q
Subject code	570
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Air travel-related outbreak of multiple SARS-CoV-2 variants.

Dhanasekaran, Vijaykrishna / Edwards, Kimberly M / Xie, Ruopeng / Gu, Haogao / Adam, Dillon C / Chang, Lydia D J / Cheuk, Sammi S Y / Gurung, Shreya / Krishnan, Pavithra / Ng, Daisy Y M / Liu, Gigi Y Z / Wan, Carrie K C / Cheng, Samuel S M / Tsang, Dominic N C / Cowling, Benjamin J / Peiris, Malik / Poon, Leo L M

Journal of travel medicine

2021 Volume 28, Issue 8

Abstract: Background: A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of > 400 ... ...

Abstract	Background: A large cluster of 59 cases were linked to a single flight with 146 passengers from New Delhi to Hong Kong in April 2021. This outbreak coincided with early reports of exponential pandemic growth in New Delhi, which reached a peak of > 400 000 newly confirmed cases on 7 May 2021. Methods: Epidemiological information including date of symptom onset, date of positive-sample detection and travel and contact history for individual cases from this flight were collected. Whole genome sequencing was performed, and sequences were classified based on the dynamic Pango nomenclature system. Maximum-likelihood phylogenetic analysis compared sequences from this flight alongside other cases imported from India to Hong Kong on 26 flights between June 2020 and April 2021, as well as sequences from India or associated with India-related travel from February to April 2021 and 1217 reference sequences. Results: Sequence analysis identified six lineages of SARS-CoV-2 belonging to two variants of concern (Alpha and Delta) and one variant of public health interest (Kappa) involved in this outbreak. Phylogenetic analysis confirmed at least three independent sub-lineages of Alpha with limited onward transmission, a superspreading event comprising 37 cases of Kappa and transmission of Delta to only one passenger. Additional analysis of another 26 flights from India to Hong Kong confirmed widespread circulation of all three variants in India since early March 2021. Conclusions: The broad spectrum of disease severity and long incubation period of SARS-CoV-2 pose a challenge for surveillance and control. As illustrated by this particular outbreak, opportunistic infections of SARS-CoV-2 can occur irrespective of variant lineage, and requiring a nucleic acid test within 72 hours of departure may be insufficient to prevent importation or in-flight transmission.
MeSH term(s)	Air Travel ; COVID-19/epidemiology ; COVID-19/transmission ; Disease Outbreaks ; Hong Kong ; Humans ; India ; Phylogeny ; Travel-Related Illness
Language	English
Publishing date	2021-09-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1212504-0
ISSN	1708-8305 ; 1195-1982
ISSN (online)	1708-8305
ISSN	1195-1982
DOI	10.1093/jtm/taab149
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Zs.A 4120: Show issues

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Article: The chromatin landscape of healthy and injured cell types in the human kidney.

Gisch, Debora L / Brennan, Michelle / Lake, Blue B / Basta, Jeannine / Keller, Mark / Ferreira, Ricardo Melo / Akilesh, Shreeram / Ghag, Reetika / Lu, Charles / Cheng, Ying-Hua / Collins, Kimberly S / Parikh, Samir V / Rovin, Brad H / Robbins, Lynn / Conklin, Kimberly Y / Diep, Dinh / Zhang, Bo / Knoten, Amanda / Barwinska, Daria /

bioRxiv : the preprint server for biology

2023

Abstract	There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. However, comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measured dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We established a comprehensive and spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we noted distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of
Language	English
Publishing date	2023-06-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.07.543965
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