Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2

Lamkiewicz, Kevin; Gomez, Luis Roger Esquivel; Kühnert, Denise; Marz, Manja

doi:10.1007/978-3-031-15640-3_9

Cited by 7 publications

(5 citation statements)

References 154 publications

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“…Coronaviruses belong to the Coronaviridae family in the order Nidovirales [3] and can be subdivided into four subfamilies, termed Alpha- , Beta- , Gamma- , and Delta-coronavirus . The host range of coronaviruses is very broad and spans several mammalian and avian hosts [4] . Coronaviruses are enveloped positive-sense single-stranded RNA viruses containing an RNA genome of approximately 30 kb.…”

Section: Coronavirusesmentioning

confidence: 99%

SARS-CoV-2 infection and its effects on the endocrine system

Steenblock

Toepfner

Beuschlein

et al. 2023

Best Practice & Research Clinical Endocrinology & Metab

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Section: Coronavirusesmentioning

confidence: 99%

SARS-CoV-2 infection and its effects on the endocrine system

Steenblock

Toepfner

Beuschlein

et al. 2023

Best Practice & Research Clinical Endocrinology & Metab

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“…SARS-CoV-2 is an enveloped single-stranded positive-sense RNA virus that belongs to the family Coronaviridae [ 85 ]. SARS-CoV-2 infects human cells expressing the Angiotensin-converting enzyme 2 (ACE2) receptor and the transmembrane serine protease 2 (TMPRSS2).…”

Section: Influenza Vaccines and Cancer-related Outcomes During Icismentioning

confidence: 99%

Vaccination for seasonal influenza, pneumococcal infection and SARS-CoV-2 in patients with solid tumors: recommendations of the Associazione Italiana di Oncologia Medica (AIOM)

Pedrazzoli¹,

Lasagna²,

Cassaniti³

et al. 2023

ESMO Open

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“…The subregions were then merged into one MSA, followed by an RNA secondary structure prediction of the full-genome alignment with a window-based approach. These steps are implemented in VeGETA using Python v3.7.12 [34,35]. Additionally, we intensively examined and slightly curated the alignment manually.…”

Section: Multiple Sequence Alignment and Rna Secondary Structure Pred...mentioning

confidence: 99%

Comprehensive Survey of Conserved RNA Secondary Structures in Full-Genome Alignment of Hepatitis C Virus

Triebel,

Lamkiewicz,

Ontiveros

et al. 2023

Preprint

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Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large “cloud” of RNA genomes which - by trial and error - comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements.Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies.Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches ofHepacivirus Care provided in the supplement.

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Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2

Cited by 7 publications

References 154 publications

SARS-CoV-2 infection and its effects on the endocrine system

SARS-CoV-2 infection and its effects on the endocrine system

Vaccination for seasonal influenza, pneumococcal infection and SARS-CoV-2 in patients with solid tumors: recommendations of the Associazione Italiana di Oncologia Medica (AIOM)

Comprehensive Survey of Conserved RNA Secondary Structures in Full-Genome Alignment of Hepatitis C Virus

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