ArticleLife (Basel, Switzerland)2021
Population Genomics Insights into the First Wave of COVID-19.
Article in Life (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- Article
- Genome-wide scans for selective sweeps using convolutional neural networks.Bioinformatics (Oxford, England) · 2023Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions.Immunoinformatics (Amsterdam, Netherlands) · 2023Review
- The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2.FEMS microbiology reviews · 2022Article
- Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program.Viruses · 2022Article
- Learning vector quantization as an interpretable classifier for the detection of SARS-CoV-2 types based on their RNA sequences.Neural computing & applications · 2022Article
- Intelligent system based comparative analysis study of SARS-CoV-2 spike protein and antigenic proteins in different types of vaccines.Beni-Suef University journal of basic and applied sciences · 2022Article
- Biological and Clinical Significance of Adaptive Evolution of Coronaviruses.Life (Basel, Switzerland) · 2021Article
- The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic.Current biology : CB · 2021Review
- Population Dynamics and Structural Effects at Short and Long Range Support the Hypothesis of the Selective Advantage of the G614 SARS-CoV-2 Spike Variant.Molecular biology and evolution · 2021Article
- A Computational Framework for Pattern Detection on Unaligned Sequences: An Application on SARS-CoV-2 Data.Frontiers in genetics · 2021Article
- Modeling a deep transfer learning framework for the classification of COVID-19 radiology dataset.PeerJ. Computer science · 2021Article
- Stability of SARS-CoV-2 phylogenies.PLoS genetics · 2020Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.