scholarly journals The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand

2020 ◽  
Author(s):  
Jemma L Geoghegan ◽  
Jordan Douglas ◽  
Xiaoyun Ren ◽  
Matthew Storey ◽  
James Hadfield ◽  
...  
Keyword(s):  
New Zealand ◽  
Genomic Data ◽  
Mitigation Strategies ◽  
Genomic Sequencing ◽  
Primary Role ◽  
Sequencing Data ◽  
Strategic Innovation ◽  
Innovation Fund ◽  
Health Research Council ◽  
First Time

SummaryBackgroundReal-time genomic sequencing has played a major role in tracking the global spread and local transmission of SARS-CoV-2, contributing greatly to disease mitigation strategies. After effectively eliminating the virus, New Zealand experienced a second outbreak of SARS-CoV-2 in August 2020. During this August outbreak, New Zealand utilised genomic sequencing in a primary role to support its track and trace efforts for the first time, leading to a second successful elimination of the virus.MethodsWe generated the genomes of 80% of the laboratory-confirmed samples of SARS-CoV-2 from New Zealand’s August 2020 outbreak and compared these genomes to the available global genomic data.FindingsGenomic sequencing was able to rapidly identify that the new COVID-19 cases in New Zealand belonged to a single cluster and hence resulted from a single introduction. However, successful identification of the origin of this outbreak was impeded by substantial biases and gaps in global sequencing data.InterpretationAccess to a broader and more heterogenous sample of global genomic data would strengthen efforts to locate the source of any new outbreaks.FundingThis work was funded by the Ministry of Health of New Zealand, New Zealand Ministry of Business, Innovation and Employment COVID-19 Innovation Acceleration Fund (CIAF-0470), ESR Strategic Innovation Fund and the New Zealand Health Research Council (20/1018 and 20/1041).

scholarly journals Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

2020 ◽  
Vol 7 ◽  
Author(s):  
Xiao Chen ◽  
Chundi Wang ◽  
Bo Pan ◽  
Borong Lu ◽  
Chao Li ◽  
...  
Keyword(s):  
Codon Usage ◽  
Single Cell ◽  
Stop Codon ◽  
Genomic Data ◽  
Evolutionary Strategy ◽  
Genomic Sequencing ◽  
Ribosomal Frameshifting ◽  
Genomic Features ◽  
First Time ◽  
Stop Codon Reassignment

Peritrichs are one of the largest groups of ciliates with over 1,000 species described so far. However, their genomic features are largely unknown. By single-cell genomic sequencing, we acquired the genomic data of three sessilid peritrichs (Cothurnia ceramicola, Vaginicola sp., and Zoothamnium sp. 2). Using genomic data from another 53 ciliates including 14 peritrichs, we reconstructed their evolutionary relationships and confirmed genome skimming as an efficient approach for expanding sampling. In addition, we profiled the stop codon usage and programmed ribosomal frameshifting (PRF) events in peritrichs for the first time. Our analysis reveals no evidence of stop codon reassignment for peritrichs, but they have prevalent +1 or -1 PRF events. These genomic features are distinguishable from other ciliates, and our observations suggest a unique evolutionary strategy for peritrichs.

scholarly journals Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

2020 ◽  
Author(s):  
Sarah Nadeau ◽  
Christiane Beckmann ◽  
Ivan Topolsky ◽  
Timothy Vaughan ◽  
Emma Hodcroft ◽  
...  
Keyword(s):  
Genomic Data ◽  
Reproductive Number ◽  
Genomic Sequencing ◽  
Epidemic Spread ◽  
Sequencing Data ◽  
Genome Sequences

AbstractPathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early viral introductions from Germany, France, and Italy and many recent introductions from Germany and France. Over the summer, we quantify the number of non-traceable infections stemming from introductions, quantify the effective reproductive number, and estimate the degree of undersampling. Our framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data.One Sentence SummaryWe quantify SARS-CoV-2 spread in Switzerland based on genome sequences from our nation-wide sequencing effort.

scholarly journals Investigating the first wave of the COVID-19 pandemic in Ukraine using epidemiological and genomic sequencing data

2021 ◽  
Author(s):  
Yuriy Gankin ◽  
Vladimir Koniukhovskii ◽  
Alina Nemira ◽  
Gerardo Chowell ◽  
Thomas A. Weppelmann ◽  
...  
Keyword(s):  
Public Health ◽  
Genomic Data ◽  
World Health ◽  
Viral Population ◽  
Genomic Sequencing ◽  
Sequencing Data ◽  
Population Number ◽  
The Public ◽  
Health Measures ◽  
The Impact

AbstractThe novel coronavirus SARS-CoV-2 emerged in China in December 2019 and has rapidly spread around the globe. The World Health Organization declared COVID-19 a pandemic in March 2020 just three months after the introduction of the virus. Individual nations have implemented and enforced with varying degrees of success a variety of social distancing interventions to slow the virus spread. Investigating the role of non-pharmaceutical interventions on COVID-19 transmission in different settings is an important research. While most transmission modeling studies have focused on the dynamics in China, neighboring Asian counties, Western Europe, and North America, there is a scarcity of studies for Eastern Europe. This study starts to fill this gap by analyzing the characteristics of the first epidemic wave in Ukraine using mathematical and statistical models together with epidemiological and genomic sequencing data. Using an agent-based model, the trajectory of the first wave in terms of cases and deaths and explore the impact of quarantine strategies via simulation studies have been characterized. The implemented stochastic model for epidemic counts suggests, that even a small delay of weeks could have increased the number of cases by up to 50%, with the potential to overwhelm hospital systems. The genomic data analysis suggests that there have been multiple introductions of SARS-CoV-2 into Ukraine during the early stages of the epidemic with eight distinct transmission clusters identified. The basic reproduction number for the epidemic has been estimated independently both from case counts data and from genomic data. The findings support the hypothesis that, the public health measures did not have a decreasing effect on the existing viral population number at the time of implementation, since strains were detected after the quarantine date. However, the public health measures did help to prevent the appearance of new (and potentially more virulent) SARS-CoV-2 variants in Ukraine.

scholarly journals Clinical Genomic Sequencing Reports in Electronic Health Record Systems Based on International Standards: Implementation Study (Preprint)

2019 ◽  
Author(s):  
Borim Ryu ◽  
Soo-Yong Shin ◽  
Rong-Min Baek ◽  
Jeong-Whun Kim ◽  
Eunyoung Heo ◽  
...  
Keyword(s):  
Electronic Health Record ◽  
Technical Specification ◽  
Genomic Data ◽  
International Standards ◽  
Practical Implementation ◽  
Genomic Sequencing ◽  
Health Record ◽  
Sequencing Data ◽  
Genomic Test ◽  
Electronic Health

BACKGROUND To implement standardized machine-processable clinical sequencing reports in an electronic health record (EHR) system, the International Organization for Standardization Technical Specification (ISO/TS) 20428 international standard was proposed for a structured template. However, there are no standard implementation guidelines for data items from the proposed standard at the clinical site and no guidelines or references for implementing gene sequencing data results for clinical use. This is a significant challenge for implementation and application of these standards at individual sites. OBJECTIVE This study examines the field utilization of genetic test reports by designing the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) for genomic data elements based on the ISO/TS 20428 standard published as the standard for genomic test reports. The goal of this pilot is to facilitate the reporting and viewing of genomic data for clinical applications. FHIR Genomics resources predominantly focus on transmitting or representing sequencing data, which is of less clinical value. METHODS In this study, we describe the practical implementation of ISO/TS 20428 using HL7 FHIR Genomics implementation guidance to efficiently deliver the required genomic sequencing results to clinicians through an EHR system. RESULTS We successfully administered a structured genomic sequencing report in a tertiary hospital in Korea based on international standards. In total, 90 FHIR resources were used. Among 41 resources for the required fields, 26 were reused and 15 were extended. For the optional fields, 28 were reused and 21 were extended. CONCLUSIONS To share and apply genomic sequencing data in both clinical practice and translational research, it is essential to identify the applicability of the standard-based information system in a practical setting. This prototyping work shows that reporting data from clinical genomics sequencing can be effectively implemented into an EHR system using the existing ISO/TS 20428 standard and FHIR resources.

scholarly journals Clinical Genomic Sequencing Reports in Electronic Health Record Systems Based on International Standards: Implementation Study

10.2196/15040 ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. e15040 ◽  
Author(s):  
Borim Ryu ◽  
Soo-Yong Shin ◽  
Rong-Min Baek ◽  
Jeong-Whun Kim ◽  
Eunyoung Heo ◽  
...  
Keyword(s):  
Electronic Health Record ◽  
Technical Specification ◽  
Genomic Data ◽  
International Standards ◽  
Practical Implementation ◽  
Genomic Sequencing ◽  
Health Record ◽  
Sequencing Data ◽  
Genomic Test ◽  
Electronic Health

Background To implement standardized machine-processable clinical sequencing reports in an electronic health record (EHR) system, the International Organization for Standardization Technical Specification (ISO/TS) 20428 international standard was proposed for a structured template. However, there are no standard implementation guidelines for data items from the proposed standard at the clinical site and no guidelines or references for implementing gene sequencing data results for clinical use. This is a significant challenge for implementation and application of these standards at individual sites. Objective This study examines the field utilization of genetic test reports by designing the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) for genomic data elements based on the ISO/TS 20428 standard published as the standard for genomic test reports. The goal of this pilot is to facilitate the reporting and viewing of genomic data for clinical applications. FHIR Genomics resources predominantly focus on transmitting or representing sequencing data, which is of less clinical value. Methods In this study, we describe the practical implementation of ISO/TS 20428 using HL7 FHIR Genomics implementation guidance to efficiently deliver the required genomic sequencing results to clinicians through an EHR system. Results We successfully administered a structured genomic sequencing report in a tertiary hospital in Korea based on international standards. In total, 90 FHIR resources were used. Among 41 resources for the required fields, 26 were reused and 15 were extended. For the optional fields, 28 were reused and 21 were extended. Conclusions To share and apply genomic sequencing data in both clinical practice and translational research, it is essential to identify the applicability of the standard-based information system in a practical setting. This prototyping work shows that reporting data from clinical genomics sequencing can be effectively implemented into an EHR system using the existing ISO/TS 20428 standard and FHIR resources.

scholarly journals GABAC: an arithmetic coding solution for genomic data

2019 ◽  
Vol 36 (7) ◽  
pp. 2275-2277 ◽  
Author(s):  
Jan Voges ◽  
Tom Paridaens ◽  
Fabian Müntefering ◽  
Liudmila S Mainzer ◽  
Brian Bliss ◽  
...  
Keyword(s):  
Genomic Data ◽  
International Organization ◽  
Arithmetic Coding ◽  
Supplementary Information ◽  
Genomic Sequencing ◽  
Command Line ◽  
Supplementary Data ◽  
Sequencing Data ◽  
Binary Arithmetic ◽  
Straightforward Solution

Abstract Motivation In an effort to provide a response to the ever-expanding generation of genomic data, the International Organization for Standardization (ISO) is designing a new solution for the representation, compression and management of genomic sequencing data: the Moving Picture Experts Group (MPEG)-G standard. This paper discusses the first implementation of an MPEG-G compliant entropy codec: GABAC. GABAC combines proven coding technologies, such as context-adaptive binary arithmetic coding, binarization schemes and transformations, into a straightforward solution for the compression of sequencing data. Results We demonstrate that GABAC outperforms well-established (entropy) codecs in a significant set of cases and thus can serve as an extension for existing genomic compression solutions, such as CRAM. Availability and implementation The GABAC library is written in C++. We also provide a command line application which exercises all features provided by the library. GABAC can be downloaded from https://github.com/mitogen/gabac. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

2021 ◽  
Author(s):  
Shilpa Nadimpalli Kobren ◽  
◽  
Dustin Baldridge ◽  
Matt Velinder ◽  
Joel B. Krier ◽  
...  
Keyword(s):  
Online Survey ◽  
Variant Calling ◽  
Theoretical Method ◽  
The United States ◽  
Genomic Sequencing ◽  
Biomedical Data ◽  
Sequencing Data ◽  
Multimodal Data ◽  
Undiagnosed Diseases ◽  
Undiagnosed Diseases Network

Abstract Purpose Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful. Methods We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols. Results We found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases. Conclusion The largest differences across diagnostic workflows suggest that advances in structural variant detection, noncoding variant interpretation, and integration of additional biomedical data may be especially promising for solving chronically undiagnosed cases.

Lecanactis (Roccellaceae) in Tasmania, with the description of a new saxicolous species and a revised key for the genus in Australia

2021 ◽  
Vol 53 (1) ◽  
pp. 95-101
Author(s):  
Gintaras Kantvilas
Keyword(s):  
New Zealand ◽  
New South ◽  
First Record ◽  
New Taxon ◽  
European Species ◽  
Australian Species ◽  
South Wales ◽  
Distribution And Ecology ◽  
Tasmanian Endemic ◽  
First Time

AbstractThe lichen genus Lecanactis Körb. in Tasmania comprises six species: L. abietina (Ach.) Körb., which is widespread and pan-temperate; L. latispora Egea & Torrente and L. neozelandica Egea & Torrente, both shared with New Zealand and with the former recorded here from the Auckland Islands for the first time; L. mollis (Stirt.) Frisch & Ertz, shared with Victoria and New Zealand; L. aff. dilleniana (Ach.) Körb., a European species recorded provisionally for Tasmania on the basis of several sterile collections; L. scopulicola Kantvilas, which is described here as new to science and apparently a Tasmanian endemic. This new taxon occurs in rocky underhangs and is characterized by a thick, leprose thallus containing schizopeltic acid, and 3-septate ascospores, 19–30 × 4.5–6 μm. Short descriptions and a discussion of distribution and ecology are given for all species. A key for all 11 Australian species of the genus is provided, including L. subfarinosa (C. Knight) Hellb. and L. tibelliana Egea & Torrente, which are recorded for Australia for the first time, and L. platygraphoides (Müll.Arg.) Zahlbr., a first record for New South Wales. Lecanactis spermatospora Egea & Torrente and L. sulphurea Egea & Torrente are also included.

Feather mites of the genera Dubininia and Cacatualges (Acari: Xolalgidae) associated with parrots (Aves: Psittaciformes) of the Old World

Zootaxa ◽  
2017 ◽  
Vol 4272 (4) ◽  
pp. 451 ◽  
Author(s):  
SERGEY V. MIRONOV ◽  
RAINER EHRNSBERGER ◽  
JACEK DABERT
Keyword(s):  
New Species ◽  
New Zealand ◽  
New Guinea ◽  
Melopsittacus Undulatus ◽  
Feather Mites ◽  
Systematic Revision ◽  
Old World ◽  
New Diagnosis ◽  
First Time

This paper gives a systematic revision of feather mites of the genera Dubininia Vassilev, 1958 and Cacatualges Dabert, Badek and Skoracki, 2007 (Xolalgidae: Ingrassiinae) associated with parrots (Aves: Psittaciformes) of the Old World. Five new species are described: Cacatualges probosciger sp. n. from Probosciger aterrimus (Gmelin) (Cacatuidae) from New Guinea, Dubininia charmosynae sp. n. from Charmosyna pulchella Gray GR (Psittaculidae) from New Guinea, D. micropsittae sp. n. from Micropsitta pusio pusio (Scaltter) (Psittaculidae) from New Guinea, D. nestori sp. n. from Nestor notabilis Gould (Strigopidae) from New Zealand, and D. pezopori sp. n. from Pezoporus wallicus (Kerr) (Psittaculidae) from Tasmania, Australia. Four previously described species of Dubininia are redescribed based on material from type hosts: D. curta (Trouessart, 1885) from Platycercus elegans (Gmelin) (Psittaculidae), D. lorina (Trouessart, 1885) from Lorius domicella (Linnaeus) (Psittaculidae), D. melopsittaci Atyeo and Gaud, 1987 from Melopsittacus undulatus (Shaw) (Psittaculidae), and D. psittacina (Trouessart, 1885) from Strigops harboptilus Gray GR (Strigopidae) from New Zealand. A new diagnosis for the genus Dubininia is provided. A key to all presently known Dubininia species is provided for the first time. 

Ready Player Two: A randomised controlled pilot trial investigating the feasibility of using games to improve healthy lifestyle knowledge in youth (9-16 years) at risk for type two diabetes. (Preprint)

2021 ◽  
Author(s):  
Ralph Maddison ◽  
Nilufar Baghaei ◽  
Amanda Jane Calder ◽  
Rinki Murphy ◽  
Varsha Parag ◽  
...  
Keyword(s):  
At Risk ◽  
New Zealand ◽  
Healthy Lifestyle ◽  
Pilot Trial ◽  
Extended Period ◽  
Trial Registration ◽  
Diabetes Knowledge ◽  
Game Play ◽  
Health Research Council ◽  
Randomised Controlled

UNSTRUCTURED Objective: To determine the comparative use and knowledge effects of two prototype serious games for health on healthy lifestyle knowledge in youth aged 9-16 years at risk for type 2 diabetes (T2D). Methods: A three-arm parallel randomized controlled pilot trial was undertaken to assess use of the game, and the effect of the game on healthy lifestyle and T2D diabetes knowledge. Participants were allocated to ‘Diabetic Jumper’ (n=7), ‘Ari and Friends’ (n=8), or a control game (n=8). All participants completed healthy lifestyle and T2D knowledge questionnaires at baseline, immediately after game play, and four weeks after game play. Game attitudes and preferences were also assessed. The primary outcome was the use of the game, specifically, the number of minutes played over four weeks. Results: There were no statistical differences in healthy lifestyle knowledge or diabetes knowledge over time or across games. Only one participant accessed the game for an extended period, playing the game for a total of 33 min over 4 weeks. Conclusion: Two prototype serious were unsuccessful at sustaining long-term play outside a clinic environment. However, the potential for these games to be used as stimulus to engage young people with healthy lifestyle and diabetes knowledge in a clinic setting should be further explored. Suggested improvements for future studies are discussed. Trial Registration: Australia New Zealand Clinical Trials Registry, ACTRN12619000380190. Registered 11 March 2019, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=377123 Funding: The trial was funded by a Health Research Council of New Zealand Feasibility grant.

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