Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Medientyp: Sonstige Veröffentlichung; E-Artikel

Titel: Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Beteiligte: Mavian, Carla [VerfasserIn]; Pond, Sergei Kosakovsky [VerfasserIn]; Marini, Simone [VerfasserIn]; Magalis, Brittany Rife [VerfasserIn]; Vandamme, Anne-Mieke [VerfasserIn]; Dellicour, Simon [VerfasserIn]; Scarpino, Samuel V. [VerfasserIn]; Houldcroft, Charlotte [VerfasserIn]; Villabona-Arenas, Julian [VerfasserIn]; Paisie, Taylor K. [VerfasserIn]; Trovão, Nídia S. [VerfasserIn]; Boucher, Christina [VerfasserIn]; Zhang, Yun [VerfasserIn]; Scheuermann, Richard H. [VerfasserIn]; Gascuel, Olivier [VerfasserIn]; Lam, Tommy Tsan-Yuk [VerfasserIn]; Suchard, Marc A. [VerfasserIn]; Abecasis, Ana [VerfasserIn]; Wilkinson, Eduan [VerfasserIn]; Oliveira, Tulio de [VerfasserIn]; Bento, Ana I. [VerfasserIn]; Schmidt, Heiko A. [VerfasserIn]; Martin, Darren [VerfasserIn]; Hadfield, James [VerfasserIn]; [...]

Erschienen: National Academy of Sciences, 2020-10-20

Sprache: Englisch

DOI: https://doi.org/10.5445/IR/1000124863; https://doi.org/10.1073/pnas.2007295117

ISSN: 0027-8424; 1091-6490

Schlagwörter: DATA processing & computer science

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Beschreibung: There is obvious interest in gaining insights into the epidemiology and evolution of the virus that has recently emerged in humans as the cause of the coronavirus disease 2019 (COVID-19) pandemic. The recent paper by Forster et al. analyzed 160 severe acute respiratory syndrome coronavirus (SARS-CoV-2) full genomes available (https://www.gisaid.org/) in early March 2020. The central claim is the identification of three main SARS-CoV-2 types, named A, B, and C, circulating in different proportions among Europeans and Americans (types A and C) and East Asians (type B). According to a median-joining network analysis, variant A is proposed to be the ancestral type because it links to the sequence of a coronavirus from bats, used as an outgroup to trace the ancestral origin of the human strains. The authors further suggest that the “ancestral Wuhan B-type virus is immunologically or environmentally adapted to a large section of the East Asian population, and may need to mutate to overcome resistance outside East Asia.” There are several serious flaws with their findings and interpretation. First, and most obviously, the sequence identity between SARS-CoV-2 and the bat virus is only 96.2%, implying that these viral genomes (which are nearly 30,000 nucleotides long) differ by more than 1,000 mutations. Such a distant outgroup is unlikely to provide a reliable root for the network. Yet, strangely, the branch to the bat virus, in figure 1 of their paper, is only 16 or 17 mutations in length. Indeed, the network seems to be misrooted, because (see their SI Appendix, figure S4) a virus from Wuhan from week 0 (24 December 2019) is portrayed as a descendant of a clade of viruses collected in weeks 1 to 9 (presumably from many places outside China), which makes no evolutionary or epidemiological sense. As for the finding of three main SARS-CoV-2 types, we must underline that finding different lineages in different countries and regions is expected with any RNA virus experiencing founder effects. According to Forster et al.’s ...

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