Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec

The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess the viral diversity of the outbreak. We report 264 viral genomes from 242 individuals (both staff and patients) with associated clinical features and outcomes, as well as longitudinal samples, technical replicates and the first publicly disseminated SARS-CoV-2 genomes in Quebec. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades that evaded supervised lineage assignment methods, including Pangolin, and identified certain symptoms (headache, myalgia and sore throat) that are significantly associated with favorable patient outcomes. We also address certain limitations of standard SARS-CoV-2 bioinformatics procedures, notably when presented with multiple viral haplotypes.

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Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes

PLoS ONE ◽

10.1371/journal.pone.0260714 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0260714

Author(s):

Bastien Paré ◽

Marieke Rozendaal ◽

Sacha Morin ◽

Léa Kaufmann ◽

Shawn M. Simpson ◽

...

Keyword(s):

Patient Outcomes ◽

Spike Protein ◽

Data Driven ◽

Nanopore Sequencing ◽

Health Records ◽

Viral Genomes ◽

Patient Health ◽

Clinical Interest ◽

Hospital Acquired ◽

Viral Lineage

The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess viral diversity (unknown at the time in Quebec) and potential associations with clinical outcomes. We report 264 viral genomes from 242 individuals–both staff and patients–with associated clinical features and outcomes, as well as longitudinal samples and technical replicates. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades with mutations of clinical interest, namely in the Spike protein, that evaded supervised lineage assignment methods–including Pangolin and NextClade supervised lineage assignment tools. We also report that certain symptoms (headache, myalgia and sore throat) are significantly associated with favorable patient outcomes. Our findings demonstrate the strength of unsupervised, data-driven analyses whilst suggesting that caution should be used when employing supervised genomic workflows, particularly during the early stages of a pandemic.

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Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

F1000Research ◽

10.12688/f1000research.24751.1 ◽

2020 ◽

Vol 9 ◽

pp. 657 ◽

Cited By ~ 1

Author(s):

Evan Bolyen ◽

Matthew R. Dillon ◽

Nicholas A. Bokulich ◽

Jason T. Ladner ◽

Brendan B. Larsen ◽

...

Keyword(s):

Software Package ◽

Tracking System ◽

Viral Diversity ◽

Data Provenance ◽

Time Geography ◽

Viral Genomes ◽

Genomic Epidemiology ◽

Rapid Accumulation ◽

Support Evaluation ◽

Random Sampling Approach

The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity. The software is modular in design so that these or future sampling approaches can be applied independently and combined (or replaced with a random sampling approach) to facilitate custom workflows and benchmarking. genome-sampler is written as a QIIME 2 plugin, ensuring that its application is fully reproducible through QIIME 2’s unique retrospective data provenance tracking system. genome-sampler can be installed in a conda environment on macOS or Linux systems. A complete default pipeline is available through a Snakemake workflow, so subsampling can be achieved using a single command. genome-sampler is open source, free for all to use, and available at https://caporasolab.us/genome-sampler. We hope that this will facilitate SARS-CoV-2 research and support evaluation of viral genome sampling approaches for genomic epidemiology.

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Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity

F1000Research ◽

10.12688/f1000research.24751.2 ◽

2020 ◽

Vol 9 ◽

pp. 657

Author(s):

Evan Bolyen ◽

Matthew R. Dillon ◽

Nicholas A. Bokulich ◽

Jason T. Ladner ◽

Brendan B. Larsen ◽

...

Keyword(s):

Software Package ◽

Tracking System ◽

Viral Diversity ◽

Data Provenance ◽

Time Geography ◽

Viral Genomes ◽

Genomic Epidemiology ◽

Rapid Accumulation ◽

Support Evaluation ◽

Random Sampling Approach

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Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

Scientific Reports ◽

10.1038/s41598-021-89361-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Myat Htut Nyunt ◽

Hnin Ohnmar Soe ◽

Kay Thi Aye ◽

Wah Wah Aung ◽

Yi Yi Kyaw ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Early Phase ◽

International Travel ◽

Health Concern ◽

Whole Genome ◽

Genome Sequences ◽

Genomic Epidemiology ◽

Local Spread ◽

Control And Prevention ◽

Local Transmission

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigated the mutational and phylogenetic analysis of 30 whole-genome sequences for the virus's genomic characteristics in the specimens collected in the early phase of the pandemic (March–June, 2020) and the sudden surge of local transmission (August–September, 2020). The four samples in the early phase of infection were B.6 lineage and located within a clade of the samples collected at the same time in Singapore and Malaysia, while five returnees by rescue flights showed the lineage B. 1.36.1 (three from India), B.1.1 (one from India) and B.1.80 (one from China). However, there was no evidence of local spread from these returnees. Further, all 19 whole-genome sequences collected in the sudden surge of local transmission showed lineage B.1.36. The surge of the second wave on SARS-CoV-2 infection was linked to the single-introduction of a variant (B.1.36) that may result from the strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

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Differential Expression of BARD1 Isoforms in Melanoma

Genes ◽

10.3390/genes12020320 ◽

2021 ◽

Vol 12 (2) ◽

pp. 320

Author(s):

Lorissa I. McDougall ◽

Ryan M. Powell ◽

Magdalena Ratajska ◽

Chi F. Lynch-Sutherland ◽

Sultana Mehbuba Hossain ◽

...

Keyword(s):

Long Range ◽

Patient Outcomes ◽

Splice Variants ◽

Significant Proportion ◽

Nanopore Sequencing ◽

Rna Seq ◽

Splice Isoforms ◽

Tissue Samples ◽

Multiple Transcripts ◽

Mrna Variants

Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified BARD1 splice variants in melanoma are warranted.

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Genomic Epidemiology of SARS-CoV-2 in Madrid, Spain, during the First Wave of the Pandemic: Fast Spread and Early Dominance by D614G Variants

Microorganisms ◽

10.3390/microorganisms9020454 ◽

2021 ◽

Vol 9 (2) ◽

pp. 454

Author(s):

Esther Viedma ◽

Elias Dahdouh ◽

José González-Alba ◽

Sara González-Bodi ◽

Laura Martínez-García ◽

...

Keyword(s):

Air Transportation ◽

European Population ◽

Viral Population ◽

Rt Pcr ◽

Viral Genomes ◽

Genomic Epidemiology ◽

International Transport ◽

Polymerase Chain ◽

Phylodynamic Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineages and the diversity of the viral population during this first epidemic wave in Madrid we sequenced 224 SARS-CoV-2 viral genomes collected from three hospitals from February to May 2020. All the known major lineages were found in this set of samples, though B.1 and B.1.5 were the most frequent ones, accounting for more than 60% of the sequences. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. The lineage composition of the viral population found in Madrid was more similar to the European population than to the publicly available Spanish data, underlining the role of Madrid as a national and international transport hub. In agreement with this, phylodynamic analysis suggested multiple independent entries before the national lockdown and air transportation restrictions.

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Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea

Viruses ◽

10.3390/v13050847 ◽

2021 ◽

Vol 13 (5) ◽

pp. 847

Author(s):

Kyungmin Park ◽

Seung-Ho Lee ◽

Jongwoo Kim ◽

Jingyeong Lee ◽

Geum-Young Lee ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Republic Of Korea ◽

Hantaan Virus ◽

Genomic Sequences ◽

Whole Genome ◽

Nanopore Sequencing ◽

Apodemus Agrarius ◽

Copy Numbers ◽

Nanopore Sequencer

Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

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Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

Journal of Clinical Microbiology ◽

10.1128/jcm.02589-14 ◽

2014 ◽

Vol 53 (1) ◽

pp. 191-200 ◽

Cited By ~ 78

Author(s):

Walter Demczuk ◽

Tarah Lynch ◽

Irene Martin ◽

Gary Van Domselaar ◽

Morag Graham ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Large Scale ◽

Epidemiological Studies ◽

23S Rrna ◽

Genome Comparison ◽

Whole Genome ◽

Content Type ◽

Genomic Epidemiology ◽

High Level ◽

Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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Whole-Genome Sequencing for Bacterial Strain Typing Using the iSeq100 Platform

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.1098 ◽

2020 ◽

Vol 41 (S1) ◽

pp. s434-s434

Author(s):

Grant Vestal ◽

Steven Bruzek ◽

Amanda Lasher ◽

Amorce Lima ◽

Suzane Silbert

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Outbreak Detection ◽

Epidemiological Surveillance ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Dna Libraries ◽

Patient Health ◽

Hospital Acquired ◽

Reference Genomes

Background: Hospital-acquired infections pose a significant threat to patient health. Laboratories are starting to consider whole-genome sequencing (WGS) as a molecular method for outbreak detection and epidemiological surveillance. The objective of this study was to assess the use of the iSeq100 platform (Illumina, San Diego, CA) for accurate sequencing and WGS-based outbreak detection using the bioMérieux EPISEQ CS, a novel cloud-based software for sequence assembly and data analysis. Methods: In total, 25 isolates, including 19 MRSA isolates and 6 ATCC strains were evaluated in this study: A. baumannii ATCC 19606, B. cepacia ATCC 25416, E. faecalis ATCC 29212, E. coli ATCC 25922, P. aeruginosa ATCC 27853 and S. aureus ATCC 25923. DNA extraction of all isolates was performed on the QIAcube (Qiagen, Hilden, Germany) using the DNEasy Ultra Clean Microbial kit extraction protocol. DNA libraries were prepared for WGS using the Nextera DNA Flex Library Prep Kit (Illumina) and sequenced at 2×150-bp on the iSeq100 according to the manufacturer’s instructions. The 19 MRSA isolates were previously characterized by the DiversiLab system (bioMérieux, France). Upon validation of the iSeq100 platform, a new outbreak analysis was performed using WGS analysis using EPISEQ CS. ATCC sequences were compared to assembled reference genomes from the NCBI GenBank to assess the accuracy of the iSeq100 platform. The FASTQ files were aligned via BowTie2 version 2.2.6 software, using default parameters, and FreeBayes version 1.1.0.46-0 was used to call homozygous single-nucleotide polymorphisms (SNPs) with a minimum coverage of 5 and an allele frequency of 0.87 using default parameters. ATCC sequences were analyzed using ResFinder version 3.2 and were compared in silico to the reference genome. Results: EPISEQ CS classified 8 MRSA isolates as unrelated and grouped 11 isolates into 2 separate clusters: cluster A (5 isolates) and cluster B (6 isolates) with similarity scores of ≥99.63% and ≥99.50%, respectively. This finding contrasted with the previous characterization by DiversiLab, which identified 3 clusters of 2, 8, and 11 isolates, respectively. The EPISEQ CS resistome data detected the mecA gene in 18 of 19 MRSA isolates. Comparative analysis of the ATCCsequences to the reference genomes showed 99.9986% concordance of SNPs and 100.00% concordance between the resistance genes present. Conclusions: The iSeq100 platform accurately sequenced the bacterial isolates and could be an affordable alternative in conjunction with EPISEQ CS for epidemiological surveillance analysis and infection prevention.Funding: NoneDisclosures: None

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Chest x-ray findings and outcomes of children with suspected ventilator .. associated pneumonia

Paediatrica Indonesiana ◽

10.14238/pi52.4.2012.233-8 ◽

2012 ◽

Vol 52 (4) ◽

pp. 233

Author(s):

Neni Sumarni ◽

Muhammad Sholeh Kosim ◽

Mohammad Supriatna ◽

Eddy Sudijanto

Keyword(s):

Retrospective Study ◽

Patient Outcomes ◽

Pulmonary Infection ◽

Ventilator Associated Pneumonia ◽

Chi Square ◽

X Ray ◽

Chest X Ray ◽

Hospital Acquired ◽

Pediatric Icu ◽

The Relationship

Background Ventilator􀁖associated pneumonia (VAP) is anosocomial infection in patients who have received mechanicalventilation (MV), either by endotracheal intubation ortracheostomy, for more than 48 hours. YAP represents 80% ofall hospital􀁖acquired pneumonias. VAP incidence varies from5.1 %􀁖33.3%. The modified clinical pulmonary infection scoreis a criteria for diagnosing suspected YAP and typically includesradiographic evidence. YAP is associated with significantmorbidity and mortality.Objective To determine the relationship between chest x􀁖rayfindings and outcomes in children Mth suspected VAP.Methods This retrospective study was held in Dr. Kariadi Hospitalfrom January - December 2010. Data was collected from medicalrecords of pediatric ICU (PICU) patients with suspected VAP.Chest x􀁖ray findings and patient outcomes were recorded. X􀁖rayfindings were assessed by the on􀁖duty radiologist. Chi square testwas used for statistical analysis.Results Subjects were 30 children consisting of 14 males and 16females. Patient outcomes were 23 patients survived and 7 patientsdied. Chest x􀁖ray findings were categorized into the followinggroups and compared to patient survivability: diffuse infiltrates76.7% (OR􀁗0.694; P􀁗0.532; 95% CI 0.102 to 4.717), localhedinfiltrates 13.3% (OR􀁗4.200; P􀁗 0.225; 95% CI 0.470 t037.49),and no infiltrates 10% (OR􀁗 1.222; P􀁗 0.436; 95% CI 0.593 to0.926). None of the x􀁖ray findings had a significant correlationto patient outcomes.Conclusion There was no significant relationship between chestx􀁖ray findings and outcomes in children with suspected VAP.[Paediatr rndones. 2012;52:233-8].

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