SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Bielejec, Filip; Baele, Guy; Vrancken, Bram; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

doi:10.1093/molbev/msw082

Cited by 441 publications

(355 citation statements)

References 11 publications

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“…To identify a subset of well‐supported migration events among 2019‐nCoV strains, we used a Bayesian stochastic search variable selection procedure with a hierarchical prior on location indicators (0‐1), which allow CTMC rates to shrink to zero with some probability, using BEAST v1.8.4 21 . Strongly supported rates of virus movement (Bayes factor > 10) were identified using SpreaD3 v0.9.6 29 …”

Section: Methodsmentioning

confidence: 99%

Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

Zai

Wang

et al. 2020

Journal of Medical Virology

159

118

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To investigate the genetic diversity, time origin, and evolutionary history of the 2019-nCoV outbreak in China and Thailand, a total of 12 genome sequences of the virus with known sampling date (24 December 2019 and 13 January 2020) and geographic location (primarily Wuhan city, Hubei Province, China, but also Bangkok, Thailand) were analyzed. Phylogenetic and likelihood-mapping analyses of these genome sequences were performed. On the basis of our results, the star-like signal and topology of 2019-nCoV may be indicative of potentially large "first generation" human-to-human virus transmission.

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Section: Methodsmentioning

confidence: 99%

Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

Zai

Wang

et al. 2020

Journal of Medical Virology

159

118

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show abstract

“…The trees were summarized in a maximum clade credibility (MCC) tree with temporal and spatial annotation using the Tree Annotator v1.8.3 software after discarding the burn-in samples. To visualize the geographic migration of the virus over the time, a keyhole markup language (KML) file was generated using SpreaD3 v0.9.6 [54], which can be visualized via Google Earth V. Monophyly was constrained for all sequences except for sequence A/eq/Uruguay/1/1963 detected in Uruguay in 1963.…”

Section: Methodsmentioning

confidence: 99%

Molecular Epidemiology and Spatio-Temporal Dynamics of the H3N8 Equine Influenza Virus in South America

et al. 2016

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Equine influenza virus (EIV) is considered the most important respiratory pathogen of horses as outbreaks of the disease lead to substantial economic losses. The H3N8 EIV has caused respiratory disease in horses across the world, including South American countries. Nucleotide and deduced amino acid sequences for the complete haemagglutinin gene of the H3N8 EIV detected in South America since 1963 were analyzed. Phylogenetic and Bayesian coalescent analyses were carried out to study the origin, the time of the most recent common ancestors (tMRCA), the demographic and the phylogeographic patterns of the H3N8 EIV. The phylogenetic analysis demonstrated that the H3N8 EIV detected in South America grouped in 5 well-supported monophyletic clades, each associated with strains of different origins. The tMRCA estimated for each group suggested that the virus was circulating in North America at least one year before its effective circulation in the South American population. Phylogenetic and coalescent analyses revealed a polyphyletic behavior of the viruses causing the outbreaks in South America between 1963 and 2012, possibly due to the introduction of at least 4 different EIVs through the international movement of horses. In addition, phylodynamic analysis suggested South America as the starting point of the spread of the H3N8 EIV in 1963 and showed migration links from the United States to South America in the subsequent EIV irruptions. Further, an increase in the relative genetic diversity was observed between 2006 and 2007 and a subsequent decline since 2009, probably due to the co-circulation of different lineages and as a result of the incorporation of the Florida clade 2 strain in vaccines, respectively. The observed data highlight the importance of epidemiological surveillance and the implementation of appropriate quarantine procedures to prevent outbreaks of the disease.

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“…For visualization purposes, we also inferred an MCC tree for viruses solely from the H1a-3 lineage (n=109). The dispersal of H1a-3 viruses from Manitoba into the United States is visualized using SpreaD3 [44] at four time points. We applied a Skyride coalescent model to infer and visualize the effective population size (Ne) dynamics of this lineage.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States

Nelson

Culhane

Trovão

et al. 2017

Journal of General Virology

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Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world's largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada's population of~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1a-3), with a two-amino acid deletion at H1 positions 146-147, that experienced rapid growth in Manitoba's swine herds during 2014-2015. H1a-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1a-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1a-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.

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SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes

Cited by 441 publications

References 11 publications

Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

Potential of large “first generation” human‐to‐human transmission of 2019‐nCoV

Molecular Epidemiology and Spatio-Temporal Dynamics of the H3N8 Equine Influenza Virus in South America

The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States

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