Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

AbstractAs the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering a new era of “genomic contact tracing” – that is, using viral genome sequences to trace local transmission dynamics. However, because the viral phylogeny is already so large – and will undoubtedly grow many fold – placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient, tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach improves the speed of phylogenetic placement of new samples and data visualization by orders of magnitude, making it possible to complete the placements under real-time constraints. Our method also provides the key ingredient for maintaining a fully-updated reference phylogeny. We make these tools available to the research community through the UCSC SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for laboratories worldwide.Software AvailabilityUSHER is available to users through the UCSC Genome Browser at https://genome.ucsc.edu/cgi-bin/hgPhyloPlace. The source code and detailed instructions on how to compile and run UShER are available from https://github.com/yatisht/usher.

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Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

10.1101/2021.11.11.21266107 ◽

2021 ◽

Author(s):

Sarah A. Nadeau ◽

Timothy G. Vaughan ◽

Christiane Beckmann ◽

Ivan Topolsky ◽

Chaoran Chen ◽

...

Keyword(s):

Transmission Dynamics ◽

Added Value ◽

Outbreak Detection ◽

Contact Tracing ◽

Sequencing Data ◽

Genome Sequences ◽

Health Measures ◽

Genome Data ◽

Transmission Chain ◽

Local Transmission

Genome sequences allow quantification of changes in case introductions from abroad and local transmission dynamics. We sequenced 11,357 SARS-CoV-2 genomes from Switzerland in 2020 - the 6th largest effort globally. Using these data, we estimated introductions and their persistence throughout 2020. By contrasting estimates with null models, we estimate at least 83% of introductions were adverted during Switzerland's border closures. Further, transmission chain persistence roughly doubled after the partial lockdown was lifted. Then, using a novel phylodynamic method, we suggest transmission in newly introduced outbreaks slowed 36 - 64% upon outbreak detection in summer 2020, but not in fall. This could indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.

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Insights into human genetic variation and population history from 929 diverse genomes

10.1101/674986 ◽

2019 ◽

Cited By ~ 12

Author(s):

Anders Bergström ◽

Shane A. McCarthy ◽

Ruoyun Hui ◽

Mohamed A. Almarri ◽

Qasim Ayub ◽

...

Keyword(s):

Genetic Variation ◽

Central Africa ◽

Population History ◽

Human Populations ◽

Genome Sequences ◽

High Coverage ◽

Geographical Regions ◽

History Of ◽

Different Populations ◽

Source Populations

AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

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Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

10.1101/2021.04.16.440141 ◽

2021 ◽

Author(s):

Jingsong Zhang ◽

Yang Zhang ◽

Junyan Kang ◽

Shuiye Chen ◽

Yongqun He ◽

...

Keyword(s):

Viral Replication ◽

Viral Genome ◽

Immune Escape ◽

Alternative Hypothesis ◽

Evolutionary Process ◽

P Value ◽

Human Populations ◽

Whole Genome ◽

Genome Sequences ◽

The United Kingdom

The presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies and surveillance strategies. Here we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7. An alternative hypothesis is that the variant was simply yet to be sampled. Notably, the SARS-CoV-2 whole genome represents a large number of potential co-mutations with very strong statistical significances (p value<E-44). In addition, we used an experimental SARS-CoV-2 reporter replicon system to introduce the dominant co-mutations NSP12_c14408t, 5'UTR_c241t, and NSP3_c3037t into the viral genome, and to monitor the effect of the mutations on viral replication. Our experimental results demonstrated that the co-mutations significantly enhanced the viral replication. The study provides valuable clues for discovering the transmission chains of variant B.1.1.7 and understanding the evolutionary process of SARS-CoV-2.

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First Local Transmission Cluster of COVID-19 in Malaysia: Public Health Response

International Journal of Travel Medicine and Global Health ◽

10.34172/ijtmgh.2020.21 ◽

2020 ◽

Vol 8 (3) ◽

pp. 124-130

Author(s):

Noor Ani Ahmad ◽

Chong Zhuo Lin ◽

Sunita Abd Rahman ◽

Muhammad Haikal bin Ghazali ◽

Ezy Eriyani Nadzari ◽

...

Keyword(s):

Public Health ◽

Index Case ◽

Contact Tracing ◽

Public Health Response ◽

Imported Case ◽

Health Response ◽

History Of ◽

Local Transmission ◽

Close Contacts ◽

Inter State

Introduction: Rapid public health response is important in controlling the transmission of coronavirus disease 2019 (COVID-19). In this study, we described the public health response taken by the Ministry of Health of Malaysia in managing the first local transmission cluster of COVID-19 related to mass-gathering and inter-state traveling to celebrate a festival. Methods: We summarized strategies implemented by the Malaysia Crisis Preparedness and Response Centre (CPRC) in managing the first local transmission of COVID-19. We collected information related to the epidemiological investigation of this cluster and described the inter-state network in managing the outbreak. Results: This first local transmission of COVID-19 in Malaysia had a history of contact with her older brother, the index case, who was the first Malaysian imported case. Only two positive cases were detected out of 59 contacts traced from the index case. Close contacts with infected person/s, inter-state movement, and public/family gatherings were identified as the sources of transmission. A large number of contacts were traced from inter-state traveling, and family gatherings during the festive season, and health consultations and treatment. Conclusion: Close contacts from inter-state movement and public/family gatherings were identified as the source of transmission. Family or public gatherings during festivals or religious events should be prohibited or controlled in COVID-19 prevalent areas. A structured surveillance system with rapid contact tracing is significant in controlling the transmission of COVID-19 in the community.

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Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2

Cell Discovery ◽

10.1038/s41421-021-00282-1 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Jingsong Zhang ◽

Yang Zhang ◽

Jun-Yan Kang ◽

Shuiye Chen ◽

Yongqun He ◽

...

Keyword(s):

United Kingdom ◽

Viral Replication ◽

Viral Genome ◽

Immune Escape ◽

Alternative Hypothesis ◽

Evolutionary Process ◽

Human Populations ◽

Whole Genome ◽

Genome Sequences ◽

The United Kingdom

AbstractThe presence of SARS-CoV-2 mutants, including the emerging variant B.1.1.7, has raised great concerns in terms of pathogenesis, transmission, and immune escape. Characterizing SARS-CoV-2 mutations, evolution, and effects on infectivity and pathogenicity is crucial to the design of antibody therapies and surveillance strategies. Here, we analyzed 454,443 SARS-CoV-2 spike genes/proteins and 14,427 whole-genome sequences. We demonstrated that the early variant B.1.1.7 may not have evolved spontaneously in the United Kingdom or within human populations. Our extensive analyses suggested that Canidae, Mustelidae or Felidae, especially the Canidae family (for example, dog) could be a possible host of the direct progenitor of variant B.1.1.7. An alternative hypothesis is that the variant was simply yet to be sampled. Notably, the SARS-CoV-2 whole-genome represents a large number of potential co-mutations. In addition, we used an experimental SARS-CoV-2 reporter replicon system to introduce the dominant co-mutations NSP12_c14408t, 5′UTR_c241t, and NSP3_c3037t into the viral genome, and to monitor the effect of the mutations on viral replication. Our experimental results demonstrated that the co-mutations significantly attenuated the viral replication. The study provides valuable clues for discovering the transmission chains of variant B.1.1.7 and understanding the evolutionary process of SARS-CoV-2.

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Insights into human genetic variation and population history from 929 diverse genomes

Science ◽

10.1126/science.aay5012 ◽

2020 ◽

Vol 367 (6484) ◽

pp. eaay5012 ◽

Cited By ~ 46

Author(s):

Anders Bergström ◽

Shane A. McCarthy ◽

Ruoyun Hui ◽

Mohamed A. Almarri ◽

Qasim Ayub ◽

...

Keyword(s):

Genetic Variation ◽

Central Africa ◽

Population History ◽

Human Populations ◽

Genome Sequences ◽

High Coverage ◽

Geographical Regions ◽

History Of ◽

Different Populations ◽

Source Populations

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

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PBrowse: A web-based platform for real-time collaborative exploration of genomic data

10.1101/068049 ◽

2016 ◽

Author(s):

Peter S. Szot ◽

Andrian Yang ◽

Xin Wang ◽

Uwe Röhm ◽

Koon Ho Wong ◽

...

Keyword(s):

Real Time ◽

Genomic Data ◽

File Sharing ◽

Genome Browser ◽

Human Interaction ◽

Supplementary Information ◽

Web Based ◽

Link Type ◽

Multiple Users ◽

Wide Range

ABSTRACTSummaryThe central task of a genome browser is to enable easy visual exploration of large genomic data to gain biological insight. Most existing genome browsers were designed for data exploration by individual users, while a few allow some limited forms of collaboration among multiple users, such as file sharing and wiki-style collaborative editing of gene annotations. Our work’s premise is that allowing sharing of genome browser views instantaneously in real-time enables the exchange of ideas and insight in a collaborative project, thus harnessing the wisdom of the crowd. PBrowse is a parallel-access real-time collaborative web-based genome browser that provides both an integrated, real-time collaborative platform and a comprehensive file sharing system. PBrowse also allows real-time track comment and has integrated group chat to facilitate interactive discussion among multiple users. Through the Distributed Annotation Server protocol, PBrowse can easily access a wide range of publicly available genomic data, such as the ENCODE data sets. We argue that PBrowse, with the re-designed user management, data management and novel collaborative layer based on Biodalliance, represents a paradigm shift from seeing genome browser merely as a tool of data visualisation to a tool that enables real-time human-human interaction and knowledge exchange in a collaborative setting.AvailabilityPBrowse is available at http://pbrowse.victorchang.edu.au, and its source code is available via the open source BSD 3 license at http://github.com/VCCRI/[email protected] InformationSupplementary video demonstrating collaborative feature of pbrowse is available in https://www.youtube.com/watch?v=ROvKXZoXiIc.

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