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Reconstructing SARS-CoV-2 infection dynamics through the phylogenetic inference of unsampled sources of infection.
Perera, Deshan; Perks, Ben; Potemkin, Michael; Liu, Andy; Gordon, Paul M K; Gill, M John; Long, Quan; van Marle, Guido.
  • Perera D; Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
  • Perks B; Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
  • Potemkin M; Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
  • Liu A; International Baccalaureate Diploma program, Sir Winston Churchill High School, Calgary, AB, Canada.
  • Gordon PMK; Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
  • Gill MJ; Department of Medicine, Cumming School of Medicine, University of Calgary and Alberta Health Services, Calgary, AB, Canada.
  • Long Q; Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
  • van Marle G; Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
PLoS One ; 16(12): e0261422, 2021.
Article in English | MEDLINE | ID: covidwho-1581744
ABSTRACT
The COVID-19 pandemic has illustrated the importance of infection tracking. The role of asymptomatic, undiagnosed individuals in driving infections within this pandemic has become increasingly evident. Modern phylogenetic tools that take into account asymptomatic or undiagnosed individuals can help guide public health responses. We finetuned established phylogenetic pipelines using published SARS-CoV-2 genomic data to examine reasonable estimate transmission networks with the inference of unsampled infection sources. The system utilised Bayesian phylogenetics and TransPhylo to capture the evolutionary and infection dynamics of SARS-CoV-2. Our analyses gave insight into the transmissions within a population including unsampled sources of infection and the results aligned with epidemiological observations. We were able to observe the effects of preventive measures in Canada's "Atlantic bubble" and in populations such as New York State. The tools also inferred the cross-species disease transmission of SARS-CoV-2 transmission from humans to lions and tigers in New York City's Bronx Zoo. These phylogenetic tools offer a powerful approach in response to both the COVID-19 and other emerging infectious disease outbreaks.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2021 Document Type: Article Affiliation country: JOURNAL.PONE.0261422

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Language: English Journal: PLoS One Journal subject: Science / Medicine Year: 2021 Document Type: Article Affiliation country: JOURNAL.PONE.0261422