CalmBelt: Rapid SARS-CoV-2 Genome Characterization for Outbreak Tracking

Background: The ongoing COVID-19 pandemic is a global health crisis caused by the spread of SARS-CoV-2. Establishing links between known cases is crucial for the containment of COVID-19. In the healthcare setting, the ability to rapidly identify potential healthcare-associated COVID-19 clusters is critical for healthcare worker and patient safety. Increasing sequencing technology accessibility has allowed routine clinical diagnostic laboratories to sequence SARS-CoV-2 in clinical samples. However, these laboratories often lack specialized informatics skills required for sequence analysis. Therefore, an on-site, intuitive sequence analysis tool that enables clinical laboratory users to analyze multiple genomes and derive clinically relevant information within an actionable timeframe is needed.Results: We propose CalmBelt, an integrated framework for on-site whole genome characterization and outbreak tracking. Nanopore sequencing technology enables on-site sequencing and construction of draft genomes for multiple SARS-CoV-2 samples within 12 h. CalmBelt's interactive interface allows users to analyse multiple SARS-CoV-2 genomes by utilizing whole genome information, collection date, and additional information such as predefined potential clusters from epidemiological investigations. CalmBelt also integrates established SARS-CoV-2 nomenclature assignments, GISAID clades and PANGO lineages, allowing users to visualize relatedness between samples together with the nomenclatures. We demonstrated multiple use cases including investigation of potential hospital transmission, mining transmission patterns in a large outbreak, and monitoring possible diagnostic-escape.Conclusions: This paper presents an on-site rapid framework for SARS-CoV-2 whole genome characterization. CalmBelt interactive web application allows non-technical users, such as routine clinical laboratory users in hospitals to determine SARS-CoV-2 variants of concern, as well as investigate the presence of potential transmission clusters. The framework is designed to be compatible with routine usage in clinical laboratories as it only requires readily available sample data, and generates information that impacts immediate infection control mitigations.

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Evolutionary relationship of the L- and M-class genome segments of bat-borne fusogenic orthoreoviruses in Malaysia and Australia

Journal of General Virology ◽

10.1099/vir.0.033498-0 ◽

2011 ◽

Vol 92 (12) ◽

pp. 2930-2936 ◽

Cited By ~ 18

Author(s):

Kenny Voon ◽

Kaw Bing Chua ◽

Meng Yu ◽

Gary Crameri ◽

Jennifer A. Barr ◽

...

Keyword(s):

Sequence Analysis ◽

Evolutionary Relationship ◽

Whole Genome ◽

Gene Products ◽

Genome Characterization ◽

Genetic Lineages ◽

Genetic Reassortment ◽

Different Strains ◽

Relationship Of

We previously described three new Malaysian orthoreoviruses designated Pulau virus, Melaka virus and Kampar virus. Melaka and Kampar viruses were shown to cause respiratory disease in humans. These viruses, together with Nelson Bay virus, isolated from Australian bats, are tentatively classified as different strains within the species Pteropine orthoreovirus (PRV), formerly known as Nelson Bay orthoreovirus, based on the small (S) genome segments. Here we report the sequences of the large (L) and medium (M) segments, thus completing the whole-genome characterization of the four PRVs. All L and M segments were highly conserved in size and sequence. Conserved functional motifs previously identified in other orthoreovirus gene products were also found in the deduced proteins encoded by the cognate segments of these viruses. Detailed sequence analysis identified two genetic lineages divided into the Australian and Malaysian PRVs, and potential genetic reassortment among the M and S segments of the three Malaysian viruses.

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30-OR: Whole Genome Sequence Analysis of Type 2 Diabetes Risk in 44,713 Humans of Diverse Ancestry in the TOPMed Study

Diabetes ◽

10.2337/db19-30-or ◽

2019 ◽

Vol 68 (Supplement 1) ◽

pp. 30-OR

Author(s):

HEATHER M. HIGHLAND ◽

JENNIFER WESSEL ◽

ALISA MANNING ◽

Keyword(s):

Type 2 Diabetes ◽

Sequence Analysis ◽

Genome Sequence ◽

Diabetes Risk ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis

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Faculty Opinions recommendation of Whole-genome characterization of chemoresistant ovarian cancer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725521376.793527273 ◽

2017 ◽

Author(s):

Katherine Fuh

Keyword(s):

Ovarian Cancer ◽

Whole Genome ◽

Genome Characterization ◽

Chemoresistant Ovarian Cancer

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423. SARS-CoV-2 NGS Assay Powered by Biotia COVID-DX Software

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.617 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S278-S279

Author(s):

Dorottya Nagy-Szakal ◽

Mara Couto-Rodriguez ◽

Joseph Barrows ◽

Heather L Wells ◽

Marilyne Debieu ◽

...

Keyword(s):

Genetic Variants ◽

Viral Genome ◽

Board Member ◽

Limit Of Detection ◽

Clinical Samples ◽

Analysis Tool ◽

Viral Titer ◽

Target Enrichment ◽

Library Preparation ◽

Software Analysis

Abstract Background COVID-19 had spread quickly, causing an international public health emergency with an alarming global shortage of COVID-19 diagnostic tests. We developed and clinically validated a next-generation sequencing (NGS)-based target enrichment assay with the COVID-DX Software tailored for the detection, characterization, and surveillance of the SARS-CoV-2 viral genome. Methods The SARS-CoV-2 NGS assay consists of components including library preparation, target enrichment, sequencing, and a COVID-DX Software analysis tool. The NGS library preparation starts with extracted RNA from nasopharyngeal (NP) swabs followed by cDNA synthesis and conversion to Illumina TruSeq-compatible libraries using the Twist Library Preparation Kit via Enzymatic Fragmentation and Unique Dual Indices (UDI). The library is then enriched for SARS-CoV-2 sequences using a panel of dsDNA biotin-labeled probes, specifically designed to target the SARS-CoV-2 genome, then sequenced on an Illumina NextSeq 550 platform. The COVID-DX Software analyzes sequence results and provides a clinically oriented report, including the presence/absence of SARS-CoV-2 for diagnostic use. An additional research use only report describes the assay performance, estimated viral titer, coverage across the viral genome, genetic variants, and phylogenetic analysis. Results The SARS-CoV-2 NGS Assay was validated on 30 positive and 30 negative clinical samples. To measure the sensitivity and specificity of the assay, the positive and negative percent agreement (PPA, NPA) was defined in comparison to an orthogonal EUA RT-PCR assay (PPA [95% CI]: 96.77% [90.56%-100%] and NPA [95% CI]: 100% [100%-100%]). Data reported using our assay defined the limit of detection to be 40 copies/ml using heat-inactivated SARS-CoV-2 viral genome in clinical matrices. In-silico analysis provided >99.9% coverage across the SARS-CoV-2 viral genome and no cross-reactivity with evolutionarily similar respiratory pathogens. Conclusion The SARS-CoV-2 NGS Assay powered by the COVID-DX Software can be used to detect the SARS-CoV-2 virus and provide additional insight into viral titer and genetic variants to track transmission, stratify risk, predict outcome and therapeutic response, and control the spread of infectious disease. Disclosures Dorottya Nagy-Szakal, MD PhD, Biotia (Employee) Mara Couto-Rodriguez, MS, Biotia (Employee) Joseph Barrows, MS, Biotia, Inc. (Employee, Shareholder) Heather L. Wells, MPH, Biotia (Consultant) Marilyne Debieu, PhD, Biotia (Employee) Courteny Hager, BS, Biotia (Employee) Kristin Butcher, MS, Twist Bioscience (Employee) Siyuan Chen, PhD, Twist Bioscience (Employee) Christopher Mason, PhD, Biotia (Board Member, Employee, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder)Twist (Other Financial or Material Support, I am CEO of Biotia and Biotia has business partnership with Twist)

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Whole-genome characterization and comparative genomics of a novel freshwater cyanobacteria species: Pseudanabaena punensis

Molecular Phylogenetics and Evolution ◽

10.1016/j.ympev.2021.107272 ◽

2021 ◽

pp. 107272

Author(s):

Kirti M. Nitnaware ◽

Kiran B. Raskar ◽

Gaurav Agarwal ◽

Ricardo A. Chávez Montes ◽

Ratan Chopra ◽

...

Keyword(s):

Comparative Genomics ◽

Whole Genome ◽

Genome Characterization

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Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-021-04185-7 ◽

2021 ◽

Author(s):

Fatma Ben Abid ◽

Clement K. M. Tsui ◽

Yohei Doi ◽

Anand Deshmukh ◽

Christi L. McElheny ◽

...

Keyword(s):

Common Species ◽

Clinical Samples ◽

Whole Genome ◽

E Coli ◽

Carbapenem Resistant ◽

Genes Encoding ◽

Encoding Genes ◽

Sequence Types ◽

Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

BMC Veterinary Research ◽

10.1186/s12917-021-02945-3 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Jacqueline King ◽

Anne Pohlmann ◽

Kamila Dziadek ◽

Martin Beer ◽

Kerstin Wernike

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Economic Losses ◽

Clinical Samples ◽

Bovine Viral Diarrhea ◽

Sequence Information ◽

Whole Genome ◽

Diarrhea Virus ◽

Viral Diarrhea ◽

Viral Loads

Abstract Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5’ untranslated region and the Npro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19–32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

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2019 novel coronavirus disease with secondary ischemic stroke: two case reports

BMC Neurology ◽

10.1186/s12883-020-02033-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Bin Fu ◽

Yun Chen ◽

Ping Li

Keyword(s):

Ischemic Stroke ◽

Acute Ischemic Stroke ◽

Clinical Laboratory ◽

Case Reports ◽

Small Vessel ◽

Vessel Occlusion ◽

Aged Patients ◽

Health Crisis ◽

Physical Examinations ◽

Novel Coronavirus

Abstract Background The COVID-19 pandemic, which broke out in Wuhan in 2019, has become the global health crisis of our time. Elderly patients with certain fundamental diseases are more likely to develop severe cases. The secondary lesion following viral infection have only rarely been reported. Case presentation We here report two cases of coronavirus-infected pneumonia with acute ischemic stroke in middle-aged patients. In both COVID-19 cases, neurological physical examinations showed normal results before infection. Lymphocytopenia, accompanied by elevated cytokines and D-dimers, were found from serum clinical laboratory examination at admission. Dysarthria and limb muscle weakness are initial manifestations, occurring one week after infect-causative pathogen, SARS-CoV-2. The head CT and head/neck arterial CTA showed small-vessel occlusion. The patients were diagnosed with coronavirus diseases with secondary acute ischemic stroke. They were treated with tirofiban and followed up with daily aspirin and atorvastatin. Conclusions These cases suggested that secondary ischemic stroke, mainly manifested as small-vessel occlusion, should be considered for COVID-19 patients and diagnosed and treated promptly.

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Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa506 ◽

2020 ◽

Vol 7 (11) ◽

Author(s):

Sarah Flohr ◽

Alban Ramette ◽

Philipp K A Agyeman ◽

Andrea Duppenthaler ◽

Cordula Scherer ◽

...

Keyword(s):

Sequence Analysis ◽

Genome Sequence ◽

Surgical Therapy ◽

Skin Infection ◽

Whole Genome Sequence ◽

Factitious Disorder ◽

Whole Genome ◽

Mycobacterium Chelonae ◽

Genome Sequence Analysis ◽

Adequate Therapy

Abstract Mycobacterium chelonae infections usually resolve with adequate therapy. We report the case of an adolescent with a chronic and progressive M chelonae infection refractory to combined antimicrobial and surgical therapy. Whole genome sequence analysis of consecutive isolates distinguished reinfection from recurrence and contributed to the diagnosis of a factitious disorder.

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