scholarly journals Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness in Egypt at El-Demerdash tertiary hospitals

2020 ◽  
Author(s):  
Sara H.A.Agwa ◽  
Hesham Elghazaly ◽  
Sarah El-Nakeep ◽  
Ahmad Moustafa ◽  
Manal H El-Sayed ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Characteristics ◽  
Severe Infection ◽  
Respiratory Illness ◽  
Morbidity And Mortality ◽  
Whole Genome ◽  
University Hospitals ◽  
First Case ◽  
Tertiary Hospitals

Abstract Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis and lung fibrosis. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain. To assess the clinical characteristics of the severe respiratory infection admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged female patient on mid-April 2020, B.1.1.7, clade GR. Co-infection (with both bacterial and viral) was most prevalent in pediatrics than adults, but mortality was higher in adults than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection. The most common bacterial infection in both adults and pediatrics was Klebsiella pneumoniae, followed by Staphylococcus aureus and Streptococcus pneumoniae. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection is the most prevalent in children and further research is needed in this area.

scholarly journals Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness in Egypt at El-Demerdash tertiary hospitals

2020 ◽  
Author(s):  
Sara H.A.Agwa ◽  
Hesham Elghazaly ◽  
Sarah El-Nakeep ◽  
Ahmad Moustafa ◽  
Manal H El-Sayed ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Characteristics ◽  
Severe Infection ◽  
Respiratory Illness ◽  
Subject Area ◽  
Morbidity And Mortality ◽  
Whole Genome ◽  
University Hospitals ◽  
First Case

Abstract Subject Area: SARS-CoV-2Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis and lung fibrosis. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain. To assess the clinical characteristics of the severe respiratory infection admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged female patient on mid-April 2020, B.1.1.7, clade GR. Co-infection (with both bacterial and viral) was most prevalent in pediatrics than adults, but mortality was higher in adults than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection. The most common bacterial infection in both adults and pediatrics was Klebsiella pneumoniae, followed by Staphylococcus aureus and Streptococcus pneumoniae. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection is the most prevalent in children and further research is needed in this area.

scholarly journals Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Nathaly M. Sweeney ◽  
Shareef A. Nahas ◽  
Sh. Chowdhury ◽  
Sergey Batalov ◽  
Michelle Clark ◽  
...  
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Disease ◽  
Congenital Heart ◽  
Cost Of Care ◽  
Morbidity And Mortality ◽  
Whole Genome ◽  
Microarray Gene

AbstractCongenital heart disease (CHD) is the most common congenital anomaly and a major cause of infant morbidity and mortality. While morbidity and mortality are highest in infants with underlying genetic conditions, molecular diagnoses are ascertained in only ~20% of cases using widely adopted genetic tests. Furthermore, cost of care for children and adults with CHD has increased dramatically. Rapid whole genome sequencing (rWGS) of newborns in intensive care units with suspected genetic diseases has been associated with increased rate of diagnosis and a net reduction in cost of care. In this study, we explored whether the clinical utility of rWGS extends to critically ill infants with structural CHD through a retrospective review of rWGS study data obtained from inpatient infants < 1 year with structural CHD at a regional children’s hospital. rWGS diagnosed genetic disease in 46% of the enrolled infants. Moreover, genetic disease was identified five times more frequently with rWGS than microarray ± gene panel testing in 21 of these infants (rWGS diagnosed 43% versus 10% with microarray ± gene panels, p = 0.02). Molecular diagnoses ranged from syndromes affecting multiple organ systems to disorders limited to the cardiovascular system. The average daily hospital spending was lower in the time period post blood collection for rWGS compared to prior (p = 0.003) and further decreased after rWGS results (p = 0.000). The cost was not prohibitive to rWGS implementation in the care of this cohort of infants. rWGS provided timely actionable information that impacted care and there was evidence of decreased hospital spending around rWGS implementation.

scholarly journals Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 108 ◽  
Author(s):  
Bruno Simon ◽  
Maxime Pichon ◽  
Martine Valette ◽  
Gwendolyne Burfin ◽  
Mathilde Richard ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Whole Genome ◽  
University Hospitals ◽  
Surveillance Network ◽  
Genetic Traits ◽  
H3n2 Influenza ◽  
The Impact

Influenza viruses cause a remarkable disease burden and significant morbidity and mortality worldwide, and these impacts vary between seasons. To understand the mechanisms associated with these differences, a comprehensive approach is needed to characterize the impact of influenza genomic traits on the burden of disease. During 2016–2017, a year with severe A(H3N2), we sequenced 176 A(H3N2) influenza genomes using next generation sequencing (NGS) for routine surveillance of circulating influenza viruses collected via the French national influenza community-based surveillance network or from patients hospitalized in the intensive care units of the University Hospitals of Lyon, France. Taking into account confounding factors, sequencing and clinical data were used to identify genomic variants and quasispecies associated with influenza severity or vaccine failure. Several amino acid substitutions significantly associated with clinical traits were found, including NA V263I and NS1 K196E which were associated with severity and co-occurred only in viruses from the 3c.2a1 clade. Additionally, we observed that intra-host diversity as a whole and on a specific set of gene segments increased with severity. These results support the use of whole genome sequencing as a tool for the identification of genetic traits associated with severe influenza in the context of influenza surveillance.

scholarly journals Whole genome sequencing of 10K patients with acute ischaemic stroke or transient ischaemic attack: design, methods and baseline patient characteristics

2020 ◽  
pp. svn-2020-000664
Author(s):  
Si Cheng ◽  
Zhe Xu ◽  
Yang Liu ◽  
Jinxi Lin ◽  
Yong Jiang ◽  
...  
Keyword(s):  
Ischaemic Stroke ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Acute Ischaemic Stroke ◽  
Transient Ischaemic Attack ◽  
Clinical Characteristics ◽  
Molecular Mechanisms ◽  
Whole Genome ◽  
Sequencing Data ◽  
Ischaemic Attack

Background and purposeStroke is the second leading cause of death worldwide and the leading cause of mortality and long-term disability in China, but its underlying risk genes and pathways are far from being comprehensively understood. We here describe the design and methods of whole genome sequencing (WGS) for 10 914 patients with acute ischaemic stroke or transient ischaemic attack from the Third China National Stroke Registry (CNSR-III).MethodsBaseline clinical characteristics of the included patients in this study were reported. DNA was extracted from white blood cells of participants. Libraries are constructed using qualified DNA, and WGS is conducted on BGISEQ-500 platform. The average depth is intended to be greater than 30× for each subject. Afterwards, Sentieon software is applied to process the sequencing data under the Genome Analysis Toolkit best practice guidance to call genotypes of single nucleotide variants (SNVs) and insertion-deletions. For each included subject, 21 fingerprint SNVs are genotyped by MassARRAY assays to verify that DNA sample and sequencing data originate from the same individual. The copy number variations and structural variations are also called for each patient. All of the genetic variants are annotated and predicted by bioinformatics software or by reviewing public databases.ResultsThe average age of the included 10 914 patients was 62.2±11.3 years, and 31.4% patients were women. Most of the baseline clinical characteristics of the 10 914 and the excluded patients were balanced.ConclusionsThe WGS data together with abundant clinical and imaging data of CNSR-III could provide opportunity to elucidate the molecular mechanisms and discover novel therapeutic targets for stroke.

scholarly journals Integrating patient and whole genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses

2017 ◽  
Author(s):  
Emily J. Goldstein ◽  
William T. Harvey ◽  
Gavin S. Wilkie ◽  
Samantha J. Shepherd ◽  
Alasdair R. MacLean ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Influenza A ◽  
Seasonal Influenza ◽  
Epidemiological Data ◽  
Respiratory Illness ◽  
Influenza Surveillance ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

AbstractGenetic surveillance of seasonal influenza is largely focused upon sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next generation sequencing technologies allows rapid and economic whole genome sequencing (WGS). Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by both methods were highly consistent and WGS provided on average >90% whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Inter-subgroup reassortants were identified (9%), including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Significant phylogenetic associations with cases of severe acute respiratory illness observed herein warrant further investigation. Severe cases were also more likely to be associated with reassortant viruses (odds ratio: 4.4 (1.3-15.5)) and occur later in the season. These results suggest that increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.

scholarly journals First case of IMP-15-producing Pseudomonas aeruginosa in Switzerland: Challenging laboratory diagnosis using whole genome sequencing (WGS)

IDCases ◽  
2020 ◽  
Vol 22 ◽  
pp. e00933
Author(s):  
Daniel Goldenberger ◽  
Danielle Vuichard-Gysin ◽  
Kathrin Herzog ◽  
Vladimira Hinić ◽  
Helena Seth-Smith ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Laboratory Diagnosis ◽  
Whole Genome ◽  
First Case

scholarly journals Identification and Whole Genome Sequencing of the First Case of Kosakonia radicincitans Causing a Human Bloodstream Infection

2017 ◽  
Vol 8 ◽  
Author(s):  
Micah D. Bhatti ◽  
Awdhesh Kalia ◽  
Pranoti Sahasrabhojane ◽  
Jiwoong Kim ◽  
David E. Greenberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Whole Genome ◽  
First Case

scholarly journals The impact of real-time whole genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks

2021 ◽  
Author(s):  
Harriet Billam ◽  
Rodric V Francis ◽  
Mitch Clarke ◽  
Carl Yates ◽  
Theocharis Tsoleridis ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Point Of Care ◽  
Patient Flow ◽  
Epidemiological Data ◽  
Control Measures ◽  
Nosocomial Transmission ◽  
Whole Genome ◽  
University Hospitals ◽  
The Impact

Background Nosocomial infections have posed a significant problem during the COVID-19 pandemic, affecting bed capacity and patient flow in hospitals. Effective infection control measures and identifying areas of highest risk is required to reduce the risk of spread to patients who are admitted with other illnesses. This is the first pandemic where whole genome sequencing (WGS) has been readily available. We demonstrate how WGS can be deployed to help identify and control outbreaks. Aims & Methods Swabs performed on patients to detect SARS-CoV-2 underwent RT-PCR on one of multiple different platforms available at Nottingham University Hospitals NHS Trust. Positive samples underwent WGS on the GridION platform using the ARTIC amplicon sequencing protocol at the University of Nottingham. Results Phylogenetic analysis from WGS and epidemiological data was used to identify an initial transmission that occurred in the admissions ward. It also showed high prevalence of asymptomatic staff infection with genetically identical viral sequences which may have contributed to the propagation of the outbreak. Actions were taken to help reduce the risk of nosocomial transmission by the introduction of rapid point of care testing in the admissions ward and introduction of portable HEPA14 filters. WGS was also used in two instances to exclude an outbreak by discerning that the phylotypes were not identical, saving time and resources. Conclusions In conjunction with accurate epidemiological data, timely WGS can identify high risk areas of nosocomial transmission, which would benefit from implementation of appropriate control measures. Conversely, WGS can disprove nosocomial transmission, validating existing control measures and maintaining clinical service, even where epidemiological data is suggestive of an outbreak.

scholarly journals Discovery of SARS-CoV-2 strain of P.1 lineage harboring K417T/ E484K / N501Y by whole genome sequencing in the city, Japan

2021 ◽  
Author(s):  
Yosuke Hirotsu ◽  
Masao Omata
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Japanese Patients ◽  
Original Strain ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Receptor Binding Domain ◽  
Cruise Ship ◽  
First Case ◽  
The City

On the February 2020, the very first case was an American female from Diamond Princess cruise ship. Since, we have confirmed 136 patients infected with coronavirus disease 2019 (COVID-19) until February 2021. Here, we conducted the whole genome sequencing analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on samples from 70 of 136 patients (51.5%). These patients were infected in Diamond Princess cruise ship (n=1), Africa (n=2), Japan (n=66) and Brazil (n=1). The viral genome sequence of a patient on the Diamond Princess cruise ship in February 2020 was similar to that of original strain found in Wuhan, China (19A clade). Four patients, including two returnees from Africa and two lived in Japan, confirmed at the end of March 2020 had sequences similar to those of lineage with D614G mutation, which was endemic in Europe (20A [n=3] and 20B [n=1] clade). The 64 Japanese patients confirmed from September 2020 to January 2021 had sequences similar to those of the currently prevalent lineage (20B [n=58] and 20C clade [n=6]). Subsequent analysis revealed three mutations (K417T/ E484K / N501Y) in the receptor binding domain of the spike protein in a man in his 40s. The sequence was identical to the P.1 lineage (also known as 20J/501Y.V3) reported in Brazil. This is the first report of SARS-CoV-2 P.1 lineage identified in the city, Japan.

scholarly journals Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Everlyn Kamau ◽  
John W. Oketch ◽  
Zaydah R. de Laurent ◽  
My V. T. Phan ◽  
Charles N. Agoti ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Stop Codon ◽  
Amino Acid Level ◽  
Respiratory Illness ◽  
Human Metapneumovirus ◽  
Clinical Samples ◽  
Whole Genome ◽  
Individual Gene

Abstract Background Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. Results We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. Conclusion This is the first genomic characterization of HMPV genomes from African patients.

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