Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

Serdari, Dora; Kostaki, Evangelia Georgia; Paraskevis, Dimitrios; Stamatakis, Alexandros; Kapli, Paschalia

doi:10.7717/peerj.7754

Cited by 3 publications

(2 citation statements)

References 63 publications

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“…It can also sample candidate delimitations via an MCMC procedure. In a recent study, we have shown that mPTP can be successfully deployed to hepatitis type B and type C virus phylogenies for classifying subtypes (Serdari et al 2019).…”

Section: Species Delimitation With Mptpmentioning

confidence: 99%

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Morel

Barbera

Czech

et al. 2020

Molecular Biology and Evolution

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145

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Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8, 736 out of all 16, 453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into sub-classes using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

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Section: Species Delimitation With Mptpmentioning

confidence: 99%

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Morel

Barbera

Czech

et al. 2020

Molecular Biology and Evolution

Self Cite

145

View full text Add to dashboard Cite

show abstract

“…It can also sample candidate delimitations via a MCMC procedure. In a recent study we have shown that mPTP can be successfully deployed to hepatitis type B and type C virus phylogenies for classifying sub-types (42). To this end, we applied mPTP to all trees in FMSA-P and SMSA-P.…”

Section: Data Preparation and Analysis Pipelinementioning

confidence: 99%

Phylogenetic analysis of SARS-CoV-2 data is difficult

Morel

Barbera

Czech

et al. 2020

Preprint

Self Cite

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Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising all virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be possible. Finally, an automatic classification of the current sequences into sub-classes based on statistical criteria is also not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.

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Ten millennia of hepatitis B virus evolution

Kocher

Papac

Barquera

et al. 2021

Science

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Ancient DNA traces the history of hepatitis B Hepatitis B virus (HBV) infections represent a worldwide human health concern. To study the history of this pathogen, Kocher et al . identified 137 human remains with detectable levels of virus dating between 400 and 10,000 years ago. Sequencing and analyses of these ancient viruses suggested a common ancestor between 12,000 and 20,000 years ago. There is no evidence indicating that HBV was present in the earliest humans as they spread out of Africa; however, HBV was likely present in human populations before farming. Furthermore, the virus was present in the Americas by about 9000 years ago, representing a lineage sister to the viral strains found in Eurasia that diverged about 20,000 years ago. —LMZ

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Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

Cited by 3 publications

References 63 publications

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Phylogenetic analysis of SARS-CoV-2 data is difficult

Ten millennia of hepatitis B virus evolution

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