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Article ; Online: Correction for Al Hefeiti et al., "Draft Genome Sequence of Bacillus cereus Strain UAEU-H3K6M1, a Bacterium with Potential Bioremediation Abilities, Isolated from Petroleum Sludge".

Al Hefeiti, Manal A / Mafofo, Joseph / Xavier, Gess Thoms / Ramaswamy, Sathishkumar / Baby, Bincy / Harilal, Divinlal / Vijayan, Ranjit / Ashraf, S Salman

Microbiology resource announcements

2018 Volume 7, Issue 10

Abstract: This corrects the article DOI: 10.1128/MRA.00856-18.]. ...

Abstract	[This corrects the article DOI: 10.1128/MRA.00856-18.].
Language	English
Publishing date	2018-09-13
Publishing country	United States
Document type	Journal Article ; Published Erratum
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.01147-18
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Draft Genome Sequence of Bacillus cereus Strain UAEU-H3K6M1, a Bacterium with Potential Bioremediation Abilities, Isolated from Petroleum Sludge.

Al Hefeiti, Manal A / Mafofo, Joseph / Xavier, Gess Thoms / Ramaswamy, Sathishkumar / Baby, Bincy / Harilal, Divinlal / Vijayan, Ranjit / Ashraf, S Salman

Microbiology resource announcements

2018 Volume 7, Issue 3

Abstract: Here, we report the draft genome sequence of Bacillus cereus strain UAEU-H3K6M1, which was isolated from petroleum sludge in the desert. It is composed of around 5.4 Mbp and has a GC content of 35%. Functional annotation and pathway modeling showed ... ...

Abstract	Here, we report the draft genome sequence of Bacillus cereus strain UAEU-H3K6M1, which was isolated from petroleum sludge in the desert. It is composed of around 5.4 Mbp and has a GC content of 35%. Functional annotation and pathway modeling showed multiple genes with potential bioremediation abilities.
Language	English
Publishing date	2018-07-26
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00856-18
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes.

Jain, Ruchi / Ramaswamy, Sathishkumar / Harilal, Divinlal / Uddin, Mohammed / Loney, Tom / Nowotny, Norbert / Alsuwaidi, Hanan / Varghese, Rupa / Deesi, Zulfa / Alkhajeh, Abdulmajeed / Khansaheb, Hamda / Alsheikh-Ali, Alawi / Abou Tayoun, Ahmad

Computational and structural biotechnology journal

2020 Volume 19, Page(s) 153–160

Abstract: Characterizing key molecular and cellular pathways involved in COVID-19 is essential for disease prognosis and management. We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify ...

Abstract	Characterizing key molecular and cellular pathways involved in COVID-19 is essential for disease prognosis and management. We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify a molecular signature associated with disease severity. Specifically, we identify globally dysregulated immune related pathways, such as cytokine-cytokine receptor signaling, complement and coagulation cascades, JAK-STAT, and TGF- β signaling pathways in all, though to a higher extent in patients with severe symptoms. The excessive release of cytokines and chemokines such as
Language	English
Publishing date	2020-12-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.12.016
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Article: Utility of clinical exome sequencing in a complex Emirati pediatric cohort.

Mahfouz, Nour Abu / Kizhakkedath, Praseetha / Ibrahim, Alia / El Naofal, Maha / Ramaswamy, Sathishkumar / Harilal, Divinlal / Qutub, Yasmeen / Uddin, Mohammed / Taylor, Alan / Alloub, Zeinab / AlBanna, Ammar / Abuhammour, Walid / Fathalla, Basil / Tayoun, Ahmad Abou

Computational and structural biotechnology journal

2020 Volume 18, Page(s) 1020–1027

Abstract: Clinical exome sequencing (CES) has become a routine diagnostic tool in several pediatric subspecialties, with a reported average diagnostic yield of ~25% in this patient poulation. The utility of CES in the United Arab Emirates (UAE) has not been ... ...

Abstract	Clinical exome sequencing (CES) has become a routine diagnostic tool in several pediatric subspecialties, with a reported average diagnostic yield of ~25% in this patient poulation. The utility of CES in the United Arab Emirates (UAE) has not been previously investigated, most likely due to the lack of the appropriate tertiary pediatric centers and diagnostic genomic facilities in this country. Here, we report, for the first time, CES findings on a multispecialty pediatric cohort in the UAE (N = 51). This cohort, which was mostly Emirati (86%; 44/51), was followed at Al Jalila Children's Hospital (AJCH), the first and only dedicated tertiary pediatric center in the country. CES demonstrates a high diagnostic yield (41%; 21/51) in this cohort, where 55% (28/51) had previous non-diagnostic genetic testing while for the remaining individuals (45%), CES was the first-tier test. Given the reported high consanguinity rate in this population, 48% of the positive cases (10/21) were due to genes associated with recessive conditions. However, 11 out of 21 positive cases (52%) were due to heterozygous pathogenic variants in genes known to cause dominantly inherited disorders, including a case with a dual diagnosis attributed to two different genes (2%; 1/51), and another case with a novel
Language	English
Publishing date	2020-04-22
Publishing country	Netherlands
Document type	Journal Article
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.04.013
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Article ; Online: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission.

Harilal, Divinlal / Ramaswamy, Sathishkumar / Loney, Tom / Suwaidi, Hanan Al / Khansaheb, Hamda / Alkhaja, Abdulmajeed / Varghese, Rupa / Deesi, Zulfa / Nowotny, Norbert / Alsheikh-Ali, Alawi / Abou Tayoun, Ahmad

Clinical chemistry

2020 Volume 66, Issue 11, Page(s) 1450–1458

Abstract: Background: With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added ... ...

Abstract	Background: With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, the practical and cost considerations of cWGS should be addressed before it is widely implemented. Methods: We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. Results: We found considerable improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome, compared to an average of 0.63% without enrichment. Consequently, an increase in genome coverage was obtained using substantially less sequencing data, enabling higher scalability and sizable cost reductions. We also demonstrated how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains. Conclusions: SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.
MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/transmission ; Costs and Cost Analysis ; Genome, Viral ; Humans ; Information Storage and Retrieval ; Pandemics ; Phylogeny ; Pneumonia, Viral/transmission ; Population Surveillance ; SARS-CoV-2 ; Whole Genome Sequencing/economics ; Whole Genome Sequencing/methods
Keywords	covid19
Language	English
Publishing date	2020-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1093/clinchem/hvaa187
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Article ; Online: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

Harilal, Divinlal / Ramaswamy, Sathishkumar / Loney, Tom / Varghese, Rupa / Deesi, Zulfa / Nowotny, Norbert / Alsheikh-Ali, Alawi / Tayoun, Ahmad Abou

bioRxiv

Abstract: Background With the gradual reopening of economies and resuming social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-PCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage ... ...

Abstract	Background With the gradual reopening of economies and resuming social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-PCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical considerations of cWGS should be addressed before it can be widely implemented. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. Results We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 95% of the sequencing reads mapped to the viral genome compared to an average of 0.7% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how this SARS-CoV-2 genome sequence can be used to determine its possible origin through phylogenetic analysis including other viral strains. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.
Keywords	covid19
Publisher	BioRxiv
Document type	Article ; Online
DOI	10.1101/2020.06.06.138339
Database	COVID19

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Article ; Online: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission

Harilal, Divinlal / Ramaswamy, Sathishkumar / Loney, Tom / Varghese, Rupa / Deesi, Zulfa / Nowotny, Norbert / Alsheikh-Ali, Alawi / Abou Tayoun, Ahmad

bioRxiv

Abstract: Background: With the gradual reopening of economies and resuming social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-PCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage ... ...

Abstract	Background: With the gradual reopening of economies and resuming social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-PCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical considerations of cWGS should be addressed before it can be widely implemented. Methods: We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. Results: We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 95% of the sequencing reads mapped to the viral genome compared to an average of 0.7% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how this SARS-CoV-2 genome sequence can be used to determine its possible origin through phylogenetic analysis including other viral strains. Conclusions: SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.
Keywords	covid19
Language	English
Publishing date	2020-06-08
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.06.06.138339
Database	COVID19

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Article: Genotype‐phenotype correlation identified a novel SARS‐CoV‐2 variant possibly linked to severe disease

Loney, Tom / Khansaheb, Hamda / Ramaswamy, Sathishkumar / Harilal, Divinlal / Deesi, Zulfa Omar / Varghese, Rupa Murthy / Belal Al Ali, Aydah / Khadeeja, Anees / Al Suwaidi, Hanan / Alkhajeh, Abdulmajeed / Mohamed AlDabal, Laila / Uddin, Mohammed / Al Faresi, Mubarak / Joshi, Madhvi / Senok, Abiola / Nowotny, Norbert / Alsheikh‐Ali, Alawi / Abou Tayoun, Ahmad

Transboundary and emerging diseases. 2022 Mar., v. 69, no. 2

2022

Abstract: The geographic location and heterogeneous multi‐ethnic population of Dubai (United Arab Emirates; UAE) provide a unique setting to explore the global molecular epidemiology of SARS‐CoV‐2 and relationship between different viral strains and disease ... ...

Abstract	The geographic location and heterogeneous multi‐ethnic population of Dubai (United Arab Emirates; UAE) provide a unique setting to explore the global molecular epidemiology of SARS‐CoV‐2 and relationship between different viral strains and disease severity. We systematically selected (i.e. every 100th individual in the central Dubai COVID‐19 database) 256 patients by age, sex, disease severity and month to provide a representative sample of laboratory‐confirmed COVID‐19 patients (nasopharyngeal swab PCR positive) during the first wave of the UAE outbreak (January to June 2020). Sociodemographic and clinical data were extracted from medical records and full SARS‐CoV‐2 genome sequences extracted from nasopharyngeal swabs were analysed. Older age was significantly associated with COVID‐19‐associated hospital admission and mortality. Overweight/obese or diabetic patients were 3–4 times more likely to be admitted to hospital and intensive care unit (ICU). Sequencing data showed multiple independent viral introductions into the UAE from Europe, Iran and Asia (29 January–18 March), and these early strains seeded significant clustering consistent with almost exclusive community‐based transmission between April and June 2020. Majority of sequenced strains (N = 60, 52%) were from the European cluster consistent with the higher infectivity rates associated with the D614G mutation carried by most strains in this cluster. A total of 986 mutations were identified in 115 genomes, 272 were unique (majority were missense, n = 134) and 20/272 mutations were novel. A missense (Q271R) and synonymous (R41R) mutation in the S and N proteins, respectively, were identified in 2/27 patients with severe COVID‐19 but not in patients with mild or moderate disease (0/86; p = .05, Fisher's Exact Test). Both patients were women (51–64 years) with no significant underlying health conditions. The same two mutations were identified in a healthy 37‐year‐old Indian man who was hospitalized in India due to COVID‐19. Our findings provide evidence for continued community‐based transmission of the European strains in the Dubai population and highlight new mutations that might be associated with severe disease in otherwise healthy adults.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; databases ; disease severity ; genome ; genotype-phenotype correlation ; hospitals ; molecular epidemiology ; mortality ; mutation ; nationalities and ethnic groups ; overweight ; pathogenicity ; Europe ; India ; Iran ; United Arab Emirates
Language	English
Dates of publication	2022-03
Size	p. 465-476.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2414822-2
ISSN	1865-1682 ; 1865-1674
ISSN (online)	1865-1682
ISSN	1865-1674
DOI	10.1111/tbed.14004
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East.

Tayoun, Ahmad Abou / Loney, Tom / Khansaheb, Hamda / Ramaswamy, Sathishkumar / Harilal, Divinlal / Deesi, Zulfa Omar / Varghese, Rupa Murthy / Al Suwaidi, Hanan / Alkhajeh, Abdulmajeed / AlDabal, Laila Mohamed / Uddin, Mohammed / Hamoudi, Rifat / Halwani, Rabih / Senok, Abiola / Hamid, Qutayba / Nowotny, Norbert / Alsheikh-Ali, Alawi

Scientific reports

2020 Volume 10, Issue 1, Page(s) 17720

Abstract: International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab ...

Abstract	International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel hub in the Middle East, we establish SARS-CoV-2 full genome sequences from the index and early COVID-19 patients in the UAE. The genome sequences are analysed in the context of virus introductions, chain of transmissions, and possible links to earlier strains from other regions of the world. Phylogenetic analysis showed multiple spatiotemporal introductions of SARS-CoV-2 into the UAE from Asia, Europe, and the Middle East during the early phase of the pandemic. We also provide evidence for early community-based transmission and catalogue new mutations in SARS-CoV-2 strains in the UAE. Our findings contribute to the understanding of the global transmission network of SARS-CoV-2.
MeSH term(s)	Adult ; Aged ; Asia/epidemiology ; Betacoronavirus/classification ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; COVID-19 ; Child ; Child, Preschool ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/virology ; Europe/epidemiology ; Female ; Humans ; Male ; Middle Aged ; Mutation ; Pandemics ; Phylogeny ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Spatio-Temporal Analysis ; Travel ; United Arab Emirates/epidemiology ; Whole Genome Sequencing ; Young Adult
Keywords	covid19
Language	English
Publishing date	2020-10-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74666-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East

Ahmad Abou Tayoun / Tom Loney / Hamda Khansaheb / Sathishkumar Ramaswamy / Divinlal Harilal / Zulfa Omar Deesi / Rupa Murthy Varghese / Hanan Al Suwaidi / Abdulmajeed Alkhajeh / Laila Mohamed AlDabal / Mohammed Uddin / Rifat Hamoudi / Rabih Halwani / Abiola Senok / Qutayba Hamid / Norbert Nowotny / Alawi Alsheikh-Ali

Scientific Reports, Vol 10, Iss 1, Pp 1-

2020 Volume 7

Abstract: Abstract International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the ... ...

Abstract	Abstract International travel played a significant role in the early global spread of SARS-CoV-2. Understanding transmission patterns from different regions of the world will further inform global dynamics of the pandemic. Using data from Dubai in the United Arab Emirates (UAE), a major international travel hub in the Middle East, we establish SARS-CoV-2 full genome sequences from the index and early COVID-19 patients in the UAE. The genome sequences are analysed in the context of virus introductions, chain of transmissions, and possible links to earlier strains from other regions of the world. Phylogenetic analysis showed multiple spatiotemporal introductions of SARS-CoV-2 into the UAE from Asia, Europe, and the Middle East during the early phase of the pandemic. We also provide evidence for early community-based transmission and catalogue new mutations in SARS-CoV-2 strains in the UAE. Our findings contribute to the understanding of the global transmission network of SARS-CoV-2.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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