ArticleGenome research2020
Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Characterization of SARS-CoV-2 different variants and related morbidity and mortality: a systematic review.European journal of medical research · 2021Pooled it
- On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching.Genome biology and evolution · 2025Article
- Methylated Reprimo Cell-Free DNA as a Non-Invasive Biomarker for Gastric Cancer.International journal of molecular sciences · 2025Article
- How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?Microorganisms · 2024Article
- Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.Cell · 2024Article
- The Use of Contact Tracing Technologies for Infection Prevention and Control Purposes in Nosocomial Settings: A Systematic Literature Review.Infectious disease reports · 2024Review
- Dispersion of SARS-CoV-2 lineage BA.5.1.25 and its descendants in Peru during two COVID-19 waves in 2022.Genomics & informatics · 2024Article
- Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.bioRxiv : the preprint server for biology · 2023Article
- Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations.Virology journal · 2023Article
- Evolutionary implications of SARS-CoV-2 vaccination for the future design of vaccination strategies.Communications medicine · 2023Review
- Emergence, spread and characterisation of the SARS-CoV-2 variant B.1.640 circulating in France, October 2021 to February 2022.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2023Article
- Positive feedback loops exacerbate the influence of superspreaders in disease transmission.iScience · 2023Article
- The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.Genome biology · 2023Article
- Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time.Viruses · 2023Article
- Modeling the heterogeneity in COVID-19's reproductive number and its impact on predictive scenarios.Journal of applied statistics · 2023Article
- Editorial: Evolutionary mechanisms of infectious diseases, volume II.Frontiers in microbiology · 2023Article
- A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations.International journal of molecular sciences · 2022Article
- Evaluation of Variant-Specific Peptides for Detection of SARS-CoV-2 Variants of Concern.Journal of proteome research · 2022Article
- Variation analysis of SARS-CoV-2 complete sequences from Iran.Future virology · 2022Article
- Ethics of genomic passports: should the genetically resistant be exempted from lockdowns and quarantines?Journal of medical ethics · 2022Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the twenty-first century. We analyzed more than 4700 SARS-CoV-2 genomes and associated metadata retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and more than 160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a rather uniform mutation occurrence along branches that could have implications for diagnostics and the design of future vaccines. Identification of the root of SARS-CoV-2 genomes is not without problems, owing to conflicting interpretations derived from either using the bat coronavirus genomes as an outgroup or relying on the sampling chronology of the SARS-CoV-2 genomes and TMRCA estimates; however, the overall scenario favors haplogroup A as the ancestral node. Phylogenetic analysis indicates a TMRCA for SARS-CoV-2 genomes dating to November 12, 2019, thus matching epidemiological records. Sub-haplogroup A2 most likely originated in Europe from an Asian ancestor and gave rise to subclade A2a, which represents the major non-Asian outbreak, especially in Africa and Europe. Multiple founder effect episodes, most likely associated with super-spreader hosts, might explain COVID-19 pandemic to a large extent.
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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.