Whole Genome Sequencing and Evolutionary Analysis of Human Respiratory Syncytial Virus A and B from Milwaukee, WI 1998-2010

ABSTRACTA viral whole-genome sequencing (WGS) strategy, based on PCR amplification followed by next-generation sequencing, was used to investigate a nosocomial respiratory syncytial virus-B (RSV-B) outbreak in a hematology-oncology and stem cell transplant unit. RSV-B genomes from 16 patients and health care workers (HCWs) suspected to be involved in the outbreak were compared to RSV-B genomes that were acquired from outpatients during the same time period but epidemiologically unrelated to the outbreak. Phylogenetic analysis of the whole genome identified a cluster of 11 patients and HCWs who had an identical RSV-B strain which was clearly distinct from strains recovered from individuals unrelated to the outbreak. Sequence variation of the glycoprotein (G) gene alone was insufficient to distinguish the outbreak strains from the outbreak-unrelated strains, thereby demonstrating that WGS is valuable for local outbreak investigation.

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High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

Journal of Clinical Microbiology ◽

10.1128/jcm.00505-15 ◽

2015 ◽

Vol 53 (8) ◽

pp. 2622-2631 ◽

Cited By ~ 33

Author(s):

Jane F. Turton ◽

Laura Wright ◽

Anthony Underwood ◽

Adam A. Witney ◽

Yuen-Ting Chan ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

United Kingdom ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sequence Type ◽

Polymorphism Analysis ◽

Whole Genome ◽

Evolutionary Analysis ◽

Accessory Gene ◽

The United Kingdom

Whole-genome sequencing (WGS) was carried out on 87 isolates of sequence type 111 (ST-111) of Pseudomonas aeruginosa collected between 2005 and 2014 from 65 patients and 12 environmental isolates from 24 hospital laboratories across the United Kingdom on an Illumina HiSeq instrument. Most isolates (73) carried VIM-2, but others carried IMP-1 or IMP-13 (5) or NDM-1 (1); one isolate had VIM-2 and IMP-18, and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters; the NDM-1 isolate was an outlier, and the IMP isolates and 6/7 MBL-negative isolates clustered separately from the main set of 73 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital likely seeded from an environmental source, requiring different control measures; isolates from 7 other hospital laboratories in London and southeast England were also included. Bayesian evolutionary analysis indicated that all the isolates shared a common ancestor dating back ∼50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (≥95%) to bacteriophage genes. WGS of widely found international lineages such as ST-111 provides the necessary resolution to inform epidemiological investigations and intervention policies.

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Functional and evolutionary analysis of Korean bob-tailed native dog using whole-genome sequencing data

Scientific Reports ◽

10.1038/s41598-017-17817-w ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 1

Author(s):

Daehwan Lee ◽

Dajeong Lim ◽

Daehong Kwon ◽

Juyeon Kim ◽

Jongin Lee ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Evolutionary Analysis ◽

Sequencing Data

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Novel and extendable genotyping system for human respiratory syncytial virus based on whole‐genome sequence analysis

Influenza and Other Respiratory Viruses ◽

10.1111/irv.12936 ◽

2021 ◽

Author(s):

Jiani Chen ◽

Xueting Qiu ◽

Vasanthi Avadhanula ◽

Samuel S. Shepard ◽

Do‐Kyun Kim ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Sequence Analysis ◽

Genome Sequence ◽

Human Respiratory Syncytial Virus ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis ◽

Syncytial Virus

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Coxsackievirus A16 in Southern Vietnam

Frontiers in Microbiology ◽

10.3389/fmicb.2021.689658 ◽

2021 ◽

Vol 12 ◽

Author(s):

Le Nguyen Truc Nhu ◽

Le Nguyen Thanh Nhan ◽

Nguyen To Anh ◽

Nguyen Thi Thu Hong ◽

Hoang Minh Tu Van ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Vaccine Development ◽

Asia Pacific ◽

Health Concern ◽

Clinical Samples ◽

Whole Genome ◽

Evolutionary Analysis ◽

Coxsackievirus A16 ◽

Outbreak Response

Background: Hand, Foot and Mouth Disease (HFMD) is a major public health concern in the Asia-Pacific region. Most recent HFMD outbreaks have been caused by enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), CVA10, and CVA6. There has been no report regarding the epidemiology and genetic diversity of CVA16 in Vietnam. Such knowledge is critical to inform the development of intervention strategies.Materials and Methods: From 2011 to 2017, clinical samples were collected from in- and outpatients enrolled in a HFMD research program conducted at three referral hospitals in Ho Chi Minh City (HCMC), Vietnam. Throat or rectal swabs positive for CVA16 with sufficient viral load were selected for whole genome sequencing and evolutionary analysis.Results: Throughout the study period, 320 CVA16 positive samples were collected from 2808 HFMD patients (11.4%). 59.4% of patients were male. The median age was 20.8 months (IQR, 14.96–31.41). Patients resided in HCMC (55.3%), Mekong Delta (22.2%), and South East Vietnam (22.5%). 10% of CVA16 infected patients had moderately severe or severe HFMD. CVA16 positive samples from 153 patients were selected for whole genome sequencing, and 66 complete genomes were obtained. Phylogenetic analysis demonstrated that Vietnamese CVA16 strains belong to a single genogroup B1a that clusters together with isolates from China, Japan, Thailand, Malaysia, France and Australia. The CVA16 strains of the present study were circulating in Vietnam some 4 years prior to its detection in HFMD cases.Conclusion: We report for the first time on the molecular epidemiology of CVA16 in Vietnam. Unlike EV-A71, which showed frequent replacement between subgenogroups B5 and C4 every 2–3 years in Vietnam, CVA16 displays a less pronounced genetic alternation with only subgenogroup B1a circulating in Vietnam since 2011. Our collective findings emphasize the importance of active surveillance for viral circulation in HFMD endemic countries, critical to informing outbreak response and vaccine development.

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Towards a unified classification for human respiratory syncytial virus genotypes

Virus Evolution ◽

10.1093/ve/veaa052 ◽

2020 ◽

Vol 6 (2) ◽

Cited By ~ 1

Author(s):

Kaat Ramaekers ◽

Annabel Rector ◽

Lize Cuypers ◽

Philippe Lemey ◽

Els Keyaerts ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Phylogenetic Trees ◽

Phylogenetic Signal ◽

Phylogenetic Reconstruction ◽

Hypervariable Region ◽

Human Respiratory Syncytial Virus ◽

Bootstrap Support ◽

Whole Genome ◽

Patristic Distance ◽

Syncytial Virus

Abstract Since the first human respiratory syncytial virus (HRSV) genotype classification in 1998, inconsistent conclusions have been drawn regarding the criteria that define HRSV genotypes and their nomenclature, challenging data comparisons between research groups. In this study, we aim to unify the field of HRSV genotype classification by reviewing the different methods that have been used in the past to define HRSV genotypes and by proposing a new classification procedure, based on well-established phylogenetic methods. All available complete HRSV genomes (>12,000 bp) were downloaded from GenBank and divided into the two subgroups: HRSV-A and HRSV-B. From whole-genome alignments, the regions that correspond to the open reading frame of the glycoprotein G and the second hypervariable region (HVR2) of the ectodomain were extracted. In the resulting partial alignments, the phylogenetic signal within each fragment was assessed. Maximum likelihood phylogenetic trees were reconstructed using the complete genome alignments. Patristic distances were calculated between all pairs of tips in the phylogenetic tree and summarized as a density plot in order to determine a cutoff value at the lowest point following the major distance peak. Our data show that neither the HVR2 fragment nor the G gene contains sufficient phylogenetic signal to perform reliable phylogenetic reconstruction. Therefore, whole-genome alignments were used to determine HRSV genotypes. We define a genotype using the following criteria: a bootstrap support of ≥70 per cent for the respective clade and a maximum patristic distance between all members of the clade of ≤0.018 substitutions per site for HRSV-A or ≤0.026 substitutions per site for HRSV-B. By applying this definition, we distinguish twenty-three genotypes within subtype HRSV-A and six genotypes within subtype HRSV-B. Applying the genotype criteria on subsampled data sets confirmed the robustness of the method.

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Novel and extendable genotyping system for Human Respiratory Syncytial Virus based on whole-genome sequence analysis

10.22541/au.162251650.01202619/v1 ◽

2021 ◽

Author(s):

Jiani Chen ◽

Xueting Qiu ◽

Samuel Shepard ◽

Do-Kyun Kim ◽

James Hixson ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Genome Sequence ◽

Vaccine Development ◽

Phylogenetic Signal ◽

Human Respiratory Syncytial Virus ◽

Whole Genome Sequence ◽

Rate Variation ◽

Whole Genome ◽

Genotype Assignment ◽

Syncytial Virus

Background: Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes and there is no consensus on RSV genotype definition. Methods: We conducted Maximum Likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were assigned by the statistical support monophyletic clusters with at least 10-year detection time from the WGS phylogeny. Results: In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the spatial and temporal distribution of each lineage. We also provided an RSV classification tool to perform RSV genotype assignment. Conclusions: This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.

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