The origin and evolution of viruses inferred from fold family structure

Mughal, Fizza; Nasir, Arshan; Caetano‐Anollés, Gustavo

doi:10.1007/s00705-020-04724-1

Cited by 29 publications

(42 citation statements)

References 85 publications

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“…In order to address these functional and evolutionary questions in full detail, one has to take advantage of the constantly increasing wealth of sequencing data from different organisms leading to the identification of a growing number and diversity of retroid elements. Here, a combination of advanced tools and methods in molecular evolution and retroviral “paleontology” of endogenous sequences and functional molecular biology/virology concepts and studies may help us gain new insights into ancient viral evolution [ 121 , 122 ].…”

Section: Interconnection and Co-evolution Of Unique Or Non-canonicmentioning

confidence: 99%

The Unique, the Known, and the Unknown of Spumaretrovirus Assembly

Lindemann

Hütter

Wei

et al. 2021

Viruses

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Within the family of Retroviridae, foamy viruses (FVs) are unique and unconventional with respect to many aspects in their molecular biology, including assembly and release of enveloped viral particles. Both components of the minimal assembly and release machinery, Gag and Env, display significant differences in their molecular structures and functions compared to the other retroviruses. This led to the placement of FVs into a separate subfamily, the Spumaretrovirinae. Here, we describe the molecular differences in FV Gag and Env, as well as Pol, which is translated as a separate protein and not in an orthoretroviral manner as a Gag-Pol fusion protein. This feature further complicates FV assembly since a specialized Pol encapsidation strategy via a tripartite Gag-genome–Pol complex is used. We try to relate the different features and specific interaction patterns of the FV Gag, Pol, and Env proteins in order to develop a comprehensive and dynamic picture of particle assembly and release, but also other features that are indirectly affected. Since FVs are at the root of the retrovirus tree, we aim at dissecting the unique/specialized features from those shared among the Spuma- and Orthoretrovirinae. Such analyses may shed light on the evolution and characteristics of virus envelopment since related viruses within the Ortervirales, for instance LTR retrotransposons, are characterized by different levels of envelopment, thus affecting the capacity for intercellular transmission.

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Section: Interconnection and Co-evolution Of Unique Or Non-canonicmentioning

confidence: 99%

The Unique, the Known, and the Unknown of Spumaretrovirus Assembly

Lindemann

Hütter

Wei

et al. 2021

Viruses

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“…The current stand is that viruses are ancient particles whose origin pre-dates the divergence of life into the three domains (super-kingdoms) (Thomas, 2019). However, earlier, Paleovirologists have proposed three major theories to explain the origin of viruses; (i) Virusfirst hypothesis or co-evolution theory (Mughal et al, 2020). This theory proposes viruses as primitive precursors of a cellular system.…”

Section: The Origin Of Virusesmentioning

confidence: 99%

“…The principle assumes that viruses existed first before cells as self-replicating particles. (ii) Degeneracy hypothesis (Mughal et al, 2020). This hypothesis proposes that viruses originate as small parasitic cells that depend on larger cells for survival, and due to extreme parasitism over a long time, these cells lost those genes that are not required for parasitic life (degenerate).…”

Section: The Origin Of Virusesmentioning

confidence: 99%

“…This hypothesis is also known as the regressive or reduction hypothesis. (iii) Escape hypothesis (Mughal et al, 2020). This hypothesis suggests a cellular origin of viruses.…”

Section: The Origin Of Virusesmentioning

confidence: 99%

“…However, viruses might have evolved from different mechanisms. The mechanism of virus evolution might be any one of the above, a combination of two or more of them (Mughal et al, 2020) or others yet to be discovered.…”

Section: The Origin Of Virusesmentioning

confidence: 99%

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Viruses, coronaviruses and COVID-19: A note for non-virology specialists

Raji¹,

Sanusi²,

Sekawi³

2021

Afr. J. Microbiol. Res.

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An outbreak of a respiratory disease with severe acute respiratory syndrome (SARS)like manifestations emerged in late December 2019 in the Wuhan city of China. The causative agent of this disease was later identified to be a novel Coronavirus. Subsequently, the disease was named coronavirus disease 2019 (COVID-19) by the World Health Organisation and later declared as a pandemic. The outbreak of COVID-19 came with many misinformation and misconceptions about viruses and the COVID-19 disease. Questions have been asked by non -virologists and the general public about what viruses are. Some wondered if viruses are living organisms or not. While some asked how big viruses are or if all viruses and the COVID-19 virus is artificially created. Yet others attributed the outbreak to the new quantum leap in the electromagnet field; the latest 5G technology. There are also concerns raised about the new virus being a bioweapon or an act of biowarfare. These numerous questions needed to be clarified concisely with available scientific knowledge. Thus, this review is providing answers to the 10 frequently asked questions aimed at informing the non -virologist in the academic field and beyond.

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The tree of life describes a tripartite cellular world

2021

Self Cite

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The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ''gaps.'' In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods.Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open.

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The origin and evolution of viruses inferred from fold family structure

Cited by 29 publications

References 85 publications

The Unique, the Known, and the Unknown of Spumaretrovirus Assembly

The Unique, the Known, and the Unknown of Spumaretrovirus Assembly

Viruses, coronaviruses and COVID-19: A note for non-virology specialists

The tree of life describes a tripartite cellular world

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