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Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries.
Waleed Aljabr; Muhannad Alruwaili; Rebekah Penrice-Randal; Abdulrahman Alrezaihi; Abbie Jasmine Harrison; Yan Ryan; Eleanor Bentley; Benjamin Jones; Bader Y. Alhatlani; Dayel AlShahrani; Zana Mahmood; Natasha Y. Rickett; Bandar Alosaimi; Asif Naeem; Saad Alamri; Hadel Alsran; Maaweya E. Hamed; Xiaofeng Dong; Abdullah M. Assiri; Abdullah R. Alrasheed; Muaawia Hamza; Miles W. Carroll; Matthew Gemmell; Alistair Darby; I’Ah Donovan-Banfield; James P. Stewart; David A. Matthews; Andrew D. Davidson; Julian A. Hiscox. Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS. mSphere 2021, 6, e0021921 .
AMA StyleWaleed Aljabr, Muhannad Alruwaili, Rebekah Penrice-Randal, Abdulrahman Alrezaihi, Abbie Jasmine Harrison, Yan Ryan, Eleanor Bentley, Benjamin Jones, Bader Y. Alhatlani, Dayel AlShahrani, Zana Mahmood, Natasha Y. Rickett, Bandar Alosaimi, Asif Naeem, Saad Alamri, Hadel Alsran, Maaweya E. Hamed, Xiaofeng Dong, Abdullah M. Assiri, Abdullah R. Alrasheed, Muaawia Hamza, Miles W. Carroll, Matthew Gemmell, Alistair Darby, I’Ah Donovan-Banfield, James P. Stewart, David A. Matthews, Andrew D. Davidson, Julian A. Hiscox. Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS. mSphere. 2021; 6 (4):e0021921.
Chicago/Turabian StyleWaleed Aljabr; Muhannad Alruwaili; Rebekah Penrice-Randal; Abdulrahman Alrezaihi; Abbie Jasmine Harrison; Yan Ryan; Eleanor Bentley; Benjamin Jones; Bader Y. Alhatlani; Dayel AlShahrani; Zana Mahmood; Natasha Y. Rickett; Bandar Alosaimi; Asif Naeem; Saad Alamri; Hadel Alsran; Maaweya E. Hamed; Xiaofeng Dong; Abdullah M. Assiri; Abdullah R. Alrasheed; Muaawia Hamza; Miles W. Carroll; Matthew Gemmell; Alistair Darby; I’Ah Donovan-Banfield; James P. Stewart; David A. Matthews; Andrew D. Davidson; Julian A. Hiscox. 2021. "Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS." mSphere 6, no. 4: e0021921.
Middle East Respiratory Syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional spill overs into humans. The severity of infection in humans is influenced by numerous factors and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are co-incident in the Middle East and a rapid way is required of sequencing MERS-CoV to derive genotype information for molecular epidemiology. Additionally, complicating factors in MERS-CoV infections are co-infections that require clinical management. The ability to rapidly characterise these infections would be advantageous. To rapidly sequence MERS-CoV, we developed an amplicon-based approach coupled to Oxford Nanopore long read length sequencing. The advantage of this approach is that insertions and deletions can be identified – which are the major drivers of genotype change in coronaviruses. This and a metagenomic approach were evaluated on clinical samples from patients with MERS. The data illustrated that whole genome or near whole genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants including deletion mutants. Whereas, the metagenomic analysis provided information of the background microbiome.
Waleed Aljabr; Muhannad Alruwaili; Rebekah Penrice-Randal; Abdulrahman Alrezaihi; Abbie Jasmine Harrison; Yan Ryan; Eleanor Bentley; Benjamin Jones; Bader Y. Alhatlani; Dayel Alshahrani; Zana Mahmood; Natasha J. Rickett; Bandar Alosaimi; Asif Naeem; Saad Alamri; Hadel Alsran; Maaweya Hamed; Xiaofeng Dong; Abdullah Assiri; Abdullah R. Alrasheed; Muaawia Hamza; Miles W. Carroll; Matthew Gemmell; Alistair Darby; I’Ah Donovan-Banfield; James P. Stewart; David A. Matthews; Andrew D. Davidson; Julian A. Hiscox. Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS). 2020, 1 .
AMA StyleWaleed Aljabr, Muhannad Alruwaili, Rebekah Penrice-Randal, Abdulrahman Alrezaihi, Abbie Jasmine Harrison, Yan Ryan, Eleanor Bentley, Benjamin Jones, Bader Y. Alhatlani, Dayel Alshahrani, Zana Mahmood, Natasha J. Rickett, Bandar Alosaimi, Asif Naeem, Saad Alamri, Hadel Alsran, Maaweya Hamed, Xiaofeng Dong, Abdullah Assiri, Abdullah R. Alrasheed, Muaawia Hamza, Miles W. Carroll, Matthew Gemmell, Alistair Darby, I’Ah Donovan-Banfield, James P. Stewart, David A. Matthews, Andrew D. Davidson, Julian A. Hiscox. Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS). . 2020; ():1.
Chicago/Turabian StyleWaleed Aljabr; Muhannad Alruwaili; Rebekah Penrice-Randal; Abdulrahman Alrezaihi; Abbie Jasmine Harrison; Yan Ryan; Eleanor Bentley; Benjamin Jones; Bader Y. Alhatlani; Dayel Alshahrani; Zana Mahmood; Natasha J. Rickett; Bandar Alosaimi; Asif Naeem; Saad Alamri; Hadel Alsran; Maaweya Hamed; Xiaofeng Dong; Abdullah Assiri; Abdullah R. Alrasheed; Muaawia Hamza; Miles W. Carroll; Matthew Gemmell; Alistair Darby; I’Ah Donovan-Banfield; James P. Stewart; David A. Matthews; Andrew D. Davidson; Julian A. Hiscox. 2020. "Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)." , no. : 1.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, particularly in the identification of emerging isolates with different pathogenic potential and to identify whether nucleotide changes in the genome will impair clinical diagnostic tools such as real-time PCR assays. Although single nucleotide polymorphisms and point mutations occur during the replication of coronaviruses, one of the biggest drivers in genetic change is recombination. This can manifest itself in insertions and/or deletions in the viral genome. Therefore, sequencing strategies that underpin molecular epidemiology and inform virus biology in patients should take these factors into account. A long amplicon/read length-based RT-PCR sequencing approach focused on the Oxford Nanopore MinION/GridION platforms was developed to identify and sequence the SARS-CoV-2 genome in samples from patients with or suspected of COVID-19. The protocol, termed Rapid Sequencing Long Amplicons (RSLAs) used random primers to generate cDNA from RNA purified from a sample from a patient, followed by single or multiplex PCRs to generate longer amplicons of the viral genome. The base protocol was used to identify SARS-CoV-2 in a variety of clinical samples and proved sensitive in identifying viral RNA in samples from patients that had been declared negative using other nucleic acid-based assays (false negative). Sequencing the amplicons revealed that a number of patients had a proportion of viral genomes with deletions.
Shona C. Moore; Rebekah Penrice-Randall; Muhannad Alruwaili; Nadine Randle; Stuart Armstrong; Catherine Hartley; Sam Haldenby; Xiaofeng Dong; Abdulrahman Alrezaihi; Mai Almsaud; Eleanor Bentley; Jordan Clark; Isabel García-Dorival; Paul Gilmore; Ximeng Han; Benjamin Jones; Lisa Luu; Parul Sharma; Ghada Shawli; Yani Sun; Qin Zhao; Steven T. Pullan; Daniel P. Carter; Kevin Bewley; Jake Dunning; En-Min Zhou; Tom Solomon; Michael Beadsworth; James Cruise; Derrick W. Crook; David A. Matthews; Andrew D. Davidson; Zana Mahmood; Waleed Aljabr; Julian Druce; Richard Vipond; Lisa Ng; Laurent Renia; Peter J. M. Openshaw; J. Kenneth Baillie; Miles W. Carroll; James Stewart; Alistair Darby; Malcolm Semple; Lance Turtle; Julian A. Hiscox. Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism. Viruses 2020, 12, 1164 .
AMA StyleShona C. Moore, Rebekah Penrice-Randall, Muhannad Alruwaili, Nadine Randle, Stuart Armstrong, Catherine Hartley, Sam Haldenby, Xiaofeng Dong, Abdulrahman Alrezaihi, Mai Almsaud, Eleanor Bentley, Jordan Clark, Isabel García-Dorival, Paul Gilmore, Ximeng Han, Benjamin Jones, Lisa Luu, Parul Sharma, Ghada Shawli, Yani Sun, Qin Zhao, Steven T. Pullan, Daniel P. Carter, Kevin Bewley, Jake Dunning, En-Min Zhou, Tom Solomon, Michael Beadsworth, James Cruise, Derrick W. Crook, David A. Matthews, Andrew D. Davidson, Zana Mahmood, Waleed Aljabr, Julian Druce, Richard Vipond, Lisa Ng, Laurent Renia, Peter J. M. Openshaw, J. Kenneth Baillie, Miles W. Carroll, James Stewart, Alistair Darby, Malcolm Semple, Lance Turtle, Julian A. Hiscox. Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism. Viruses. 2020; 12 (10):1164.
Chicago/Turabian StyleShona C. Moore; Rebekah Penrice-Randall; Muhannad Alruwaili; Nadine Randle; Stuart Armstrong; Catherine Hartley; Sam Haldenby; Xiaofeng Dong; Abdulrahman Alrezaihi; Mai Almsaud; Eleanor Bentley; Jordan Clark; Isabel García-Dorival; Paul Gilmore; Ximeng Han; Benjamin Jones; Lisa Luu; Parul Sharma; Ghada Shawli; Yani Sun; Qin Zhao; Steven T. Pullan; Daniel P. Carter; Kevin Bewley; Jake Dunning; En-Min Zhou; Tom Solomon; Michael Beadsworth; James Cruise; Derrick W. Crook; David A. Matthews; Andrew D. Davidson; Zana Mahmood; Waleed Aljabr; Julian Druce; Richard Vipond; Lisa Ng; Laurent Renia; Peter J. M. Openshaw; J. Kenneth Baillie; Miles W. Carroll; James Stewart; Alistair Darby; Malcolm Semple; Lance Turtle; Julian A. Hiscox. 2020. "Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism." Viruses 12, no. 10: 1164.
The COVID-19 pandemic is spreading at unprecedented pace among the Middle East and neighboring countries. This region is geographically, economically, politically, culturally and religiously a very sensitive area, which impose unique challenges for effective control of this epidemic. These challenges include compromised healthcare systems, prolonged regional conflicts and humanitarian crises, suboptimal levels of transparency and cooperation, and frequent religious gatherings. These factors are interrelated and collectively determine the response to the pandemic in this region. Here, we in-depth emphasize these challenges and take a glimpse of possible solutions towards mitigating the spread of COVID-19.
Zulqarnain Baloch; Zhongren Ma; Yunpeng Ji; Mohsen Ghanbari; Qiuwei Pan; Waleed Aljabr. Unique challenges to control the spread of COVID-19 in the Middle East. Journal of Infection and Public Health 2020, 13, 1247 -1250.
AMA StyleZulqarnain Baloch, Zhongren Ma, Yunpeng Ji, Mohsen Ghanbari, Qiuwei Pan, Waleed Aljabr. Unique challenges to control the spread of COVID-19 in the Middle East. Journal of Infection and Public Health. 2020; 13 (9):1247-1250.
Chicago/Turabian StyleZulqarnain Baloch; Zhongren Ma; Yunpeng Ji; Mohsen Ghanbari; Qiuwei Pan; Waleed Aljabr. 2020. "Unique challenges to control the spread of COVID-19 in the Middle East." Journal of Infection and Public Health 13, no. 9: 1247-1250.
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a lethal zoonotic pathogen circulating in the Arabian Peninsula since 2012. There is no vaccine for MERS and anti-viral treatment is generally not applicable. We investigated the evolution of the MERS-CoV spike gene sequences and changes in viral loads over time from patients in Saudi Arabia from 2015–2017. All the MERS-CoV strains belonged to lineage 5, and showed high sequence homology (99.9%) to 2017 strains. Recombination analysis showed a potential recombination event in study strains from patients in Saudi Arabia. The spike gene showed eight amino acid substitutions, especially between the A1 and B5 lineage, and contained positively selected codon 1020. We also determined that the viral loads were significantly (p < 0.001) higher in fatal cases, and virus shedding was prolonged in some fatal cases beyond 21 days. The viral concentration peaked during the first week of illness, and the lower respiratory specimens had higher levels of MERS-CoV RNA. The presence of the diversifying selection and the topologies with the structural mapping of residues under purifying selection suggested that codon 1020 might have a role in the evolution of spike gene during the divergence of different lineages. This study will improve our understanding of the evolution of MERS-CoV, and also highlights the need for enhanced surveillance in humans and dromedaries. The presence of amino acid changes at the N-terminal domain and structural mapping of residues under positive selection at heptad repeat 1 provides better insight into the adaptive evolution of the spike gene and might have a potential role in virus-host tropism and pathogenesis.
Asif Naeem; Maaweya E. Hamed; Majed F. Alghoribi; Waleed Aljabr; Hadel Alsaran; Mushira A. Enani; Bandar Alosaimi. Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses 2020, 12, 502 .
AMA StyleAsif Naeem, Maaweya E. Hamed, Majed F. Alghoribi, Waleed Aljabr, Hadel Alsaran, Mushira A. Enani, Bandar Alosaimi. Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses. 2020; 12 (5):502.
Chicago/Turabian StyleAsif Naeem; Maaweya E. Hamed; Majed F. Alghoribi; Waleed Aljabr; Hadel Alsaran; Mushira A. Enani; Bandar Alosaimi. 2020. "Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)." Viruses 12, no. 5: 502.
COVID-19 is a complex disease phenotype where the underlying microbiome could influence morbidity and mortality. Amplicon and metagenomic MinION based sequencing was used to rapidly (within 8 hours) identify SARS-CoV-2 and assess the microbiome in nasopharyngeal swabs obtained from patients with COVID-19 by the ISARIC 4C consortium.
Shona C. Moore; Rebekah Penrice-Randal; Muhannad Alruwaili; Xiaofeng Dong; Steven T. Pullan; Daniel P. Carter; Kevin Bewley; Qin Zhao; Yani Sun; Catherine Hartley; En-Min Zhou; Tom Solomon; Michael B. J. Beadsworth; James Cruise; Debby Bogaert; Derrick W T Crook; David A. Matthews; Andrew D. Davidson; Zana Mahmood; Waleed Aljabr; Julian Druce; Richard T. Vipond; Lisa F. P. Ng; Laurent Renia; Peter J. M. Openshaw; J. Kenneth Baillie; Miles W. Carroll; Malcolm G. Semple; Lance Turtle; Julian Alexander Hiscox. Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19. 2020, 1 .
AMA StyleShona C. Moore, Rebekah Penrice-Randal, Muhannad Alruwaili, Xiaofeng Dong, Steven T. Pullan, Daniel P. Carter, Kevin Bewley, Qin Zhao, Yani Sun, Catherine Hartley, En-Min Zhou, Tom Solomon, Michael B. J. Beadsworth, James Cruise, Debby Bogaert, Derrick W T Crook, David A. Matthews, Andrew D. Davidson, Zana Mahmood, Waleed Aljabr, Julian Druce, Richard T. Vipond, Lisa F. P. Ng, Laurent Renia, Peter J. M. Openshaw, J. Kenneth Baillie, Miles W. Carroll, Malcolm G. Semple, Lance Turtle, Julian Alexander Hiscox. Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19. . 2020; ():1.
Chicago/Turabian StyleShona C. Moore; Rebekah Penrice-Randal; Muhannad Alruwaili; Xiaofeng Dong; Steven T. Pullan; Daniel P. Carter; Kevin Bewley; Qin Zhao; Yani Sun; Catherine Hartley; En-Min Zhou; Tom Solomon; Michael B. J. Beadsworth; James Cruise; Debby Bogaert; Derrick W T Crook; David A. Matthews; Andrew D. Davidson; Zana Mahmood; Waleed Aljabr; Julian Druce; Richard T. Vipond; Lisa F. P. Ng; Laurent Renia; Peter J. M. Openshaw; J. Kenneth Baillie; Miles W. Carroll; Malcolm G. Semple; Lance Turtle; Julian Alexander Hiscox. 2020. "Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19." , no. : 1.
The aim of this study was to evaluate the seroprevalence of hepatitis E virus (HEV), a major public health issue worldwide with the potential for transmission via blood transfusion, in blood donors in the Qassim Region, Saudi Arabia. Serum samples (n = 1,078) were collected from volunteer blood donors from January to April 2019 and tested for the presence of anti-HEV IgG and IgM by indirect enzyme-linked immunosorbent assays. Overall, the seroprevalence of anti-HEV IgG and IgM among blood donors was 5.7% and 1.3%, respectively. Additionally, the seropositive rates of anti-HEV IgG and IgM were significantly higher in non-Saudi donors (22.1% and 7.8%) than in Saudi donors (3% and 0.2%). The seroprevalence of anti-HEV IgG increased with age; however, there was no correlation between gender and anti-HEV IgG and/or IgM. The seroprevalence of HEV among blood donors in the Qassim Region was lower than previous estimates for other regions of the country. Further studies covering a wider geographical area are needed to validate and expand the findings and to determine the importance of HEV screening in the region.
Bader Y. Alhatlani; Waleed A. Aljabr; Mohammed S. Almarzouqi; Sami M. Alhatlani; Rayan N. Alzunaydi; Abeer S. Alsaykhan; Sulaiman H. Almaiman; Ahmed A. Aleid; Ammar H. Alsughayir; Yara E. Bishawri; Abdulrahman A. Almusallam. Seroprevalence of the hepatitis E virus among blood donors in the Qassim Region, Saudi Arabia. 2019, 1 .
AMA StyleBader Y. Alhatlani, Waleed A. Aljabr, Mohammed S. Almarzouqi, Sami M. Alhatlani, Rayan N. Alzunaydi, Abeer S. Alsaykhan, Sulaiman H. Almaiman, Ahmed A. Aleid, Ammar H. Alsughayir, Yara E. Bishawri, Abdulrahman A. Almusallam. Seroprevalence of the hepatitis E virus among blood donors in the Qassim Region, Saudi Arabia. . 2019; ():1.
Chicago/Turabian StyleBader Y. Alhatlani; Waleed A. Aljabr; Mohammed S. Almarzouqi; Sami M. Alhatlani; Rayan N. Alzunaydi; Abeer S. Alsaykhan; Sulaiman H. Almaiman; Ahmed A. Aleid; Ammar H. Alsughayir; Yara E. Bishawri; Abdulrahman A. Almusallam. 2019. "Seroprevalence of the hepatitis E virus among blood donors in the Qassim Region, Saudi Arabia." , no. : 1.
Human respiratory syncytial virus (HRSV) is a major cause of pediatric infection and also causes disease in the elderly and those with underlying respiratory problems. There is no vaccine for HRSV and anti-viral therapeutics are not broadly applicable. To investigate the effect of HRSV biology in children, nasopharyngeal aspirates were taken from children with different viral loads and a combined high throughput RNAseq and label free quantitative proteomics approach was used to characterize the nucleic acid and proteins in these samples. HRSV proteins were identified in the nasopharyngeal aspirates from infected children, and their abundance correlated with viral load (Ct value), confirming HRSV infection. Analysis of the HRSV genome indicated that the children were infected with sub-group A virus and that minor variants in nucleotide frequency occurred in discrete clusters along the HRSV genome, and within a patient clustered distinctly within the glycoprotein gene. Data from the samples were binned into four groups; no-HRSV infection (control), high viral load (Ct < 20), medium viral load (Ct = 20-25), and low viral load (Ct > 25). Cellular proteins associated with the anti-viral response (e.g., ISG15) were identified in the nasopharyngeal aspirates and their abundance was correlated with viral load. These combined approaches have not been used before to study HRSV biology in vivo and can be readily applied to the study the variation of virus host interactions.
Waleed Aljabr; Stuart Armstrong; Natasha Y. Rickett; Georgios Pollakis; Olivier Touzelet; Elaine Cloutman-Green; David A. Matthews; Julian A. Hiscox. High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo. Viruses 2019, 11, 926 .
AMA StyleWaleed Aljabr, Stuart Armstrong, Natasha Y. Rickett, Georgios Pollakis, Olivier Touzelet, Elaine Cloutman-Green, David A. Matthews, Julian A. Hiscox. High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo. Viruses. 2019; 11 (10):926.
Chicago/Turabian StyleWaleed Aljabr; Stuart Armstrong; Natasha Y. Rickett; Georgios Pollakis; Olivier Touzelet; Elaine Cloutman-Green; David A. Matthews; Julian A. Hiscox. 2019. "High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo." Viruses 11, no. 10: 926.