Coronaviruses

doi:10.1007/978-1-4939-2438-7

Cited by 128 publications

(35 citation statements)

References 5 publications

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“…The size of the ssRNA genome of SARS-CoV-2 is 29,891 nucleotides, it encodes 9860 amino acids and is characterized by nucleotide identity of ~ 89% with bat SARS-related-CoV SL-ZXC21 and ~ 82% with human SARS-CoVs BJ01 2003 and Tor2 [9]. CoVs are enveloped positive-sense RNA viruses, which are characterized by a very large non-segmented RNA genome (26 to 32kb length), ready to be translated [2], [5]. The genes arrangement on the SARS-CoV-2 genome is: [9].…”

Section: Similarly To Sars Epidemiological Links Between the Majoritmentioning

confidence: 99%

“…Coronaviruses (CoVs), considered to be the largest group of viruses, belong to the Nidovirales order, Coronaviridae family and Coronavirinae subfamily, which is further subdivided into four genera, the alpha-and betacoronaviruses, which infect mammalian species and gamma-and deltacoronaviruses infecting mainly birds [1], [2]. Small mammals (mice, dogs, cats) serve as reservoirs for HCoVs, with significant diversity seen in bats, which are considered to be primordial hosts of HCoVs [3].…”

Section: Introductionmentioning

confidence: 99%

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SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

Karamitros

Papadopoulou

Bousali

et al. 2020

Preprint

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In December 2019, an outbreak of atypical pneumonia (Coronavirus disease 2019 -COVID-19) associated with a novel coronavirus (SARS-CoV-2) was reported in Wuhan city, Hubei province, China. The outbreak was traced to a seafood wholesale market and human to human transmission was confirmed. The rapid spread and the death toll of the new epidemic warrants immediate intervention. The intra-host genomic variability of SARS-CoV-2 plays a pivotal role in the development of effective antiviral agents and vaccines, but also in the design of accurate diagnostics.We analyzed NGS data derived from clinical samples of three Chinese patients infected with SARS-CoV-2, in order to identify small-and large-scale intra-host variations in the viral genome. We identified tens of low-or higher-frequency single nucleotide variations (SNVs) with variable density across the viral genome, affecting 7 out of 10 protein-coding viral genes. The majority of these SNVs corresponded to missense changes. The annotation of the identified SNVs but also of all currently circulating strain variations revealed colocalization of intra-host but also strain specific SNVs with primers and probes currently used in molecular diagnostics assays. Moreover, we de-novo assembled the viral genome, in order to isolate and validate intra-host structural variations and recombination breakpoints. The bioinformatics analysis disclosed genomic rearrangements over poly-A / poly-U regions located in ORF1ab and spike (S) gene, including a potential recombination hot-spot within S gene.Our results highlight the intra-host genomic diversity and plasticity of SARS-CoV-2, pointing out genomic regions that are prone to alterations. The isolated SNVs and genomic rearrangements, reflect the intra-patient capacity of the polymorphic quasispecies, which may arise rapidly during the outbreak, allowing immunological escape of the virus, offering resistance to anti-viral drugs and affecting the sensitivity of the molecular diagnostics assays.(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.

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Section: Similarly To Sars Epidemiological Links Between the Majoritmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

Karamitros

Papadopoulou

Bousali

et al. 2020

Preprint

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“…The pandemia is still continuing and the possibility of return of new disease waves is considered to be very high. The development of efficient medications and vaccines against coronaviruses needs the knowledge of main molecular mechanisms in the virus life cycle and virus-host interaction (Maier et al, 2015;Ziebuhr, 2016;Fung & Liu, 2019;Saxena, 2020;Feng et al, 2020;Xie & Chen, 2020). In this paper we will discuss a specific interaction between nucleocapsid (N) proteins and genomic ssRNA in the coronaviruses SARS-CoV and SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting

Chechetkin

Lobzin

2020

Journal of Biomolecular Structure and Dynamics

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The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Such signals coordinated with the nucleocapsid helical structure were detected and reconstructed in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2. The main period of the signals for both viruses was about 54 nt, that implies 6.75 nt per N protein. The complete coverage of ssRNA genome of length about 30,000 nt by the nucleocapsid would need 4,400 N proteins, that makes them the most abundant among the structural proteins. The repertoires of motifs for SARS-CoV and SARS-CoV-2 were divergent but nearly coincided for different isolates of SARS-CoV-2. We obtained the distributions of assembly/packaging signals over the genomes with non-overlapping windows of width 432 nt. Finally, using the spectral entropy, we compared the load from point mutations and indels during virus age for SARS-CoV and SARS-CoV-2. We found the higher mutational load on SARS-CoV. In this sense, SARS-CoV-2 can be treated as a "newborn" virus. These observations may be helpful in practical medical applications and are of basic interest.

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“…Their genome size is about 30 kilobases (kb) which consist of non-structural open reading frames (ORFs) near the 5′-end and at least four structural proteins near the 3′-end, including membrane (M), envelope (E), spike (S), and nucleocapsid (N) proteins. The coronavirus name derives from their solar corona appearance, which is formed due to the club-shaped spikes that project from the surface of the virion [1][2][3][4].…”

Section: Introductionmentioning

confidence: 99%

“…SARS outbreak involved 29 countries, infected over 8000 people, and caused 774 deaths (the fatality rate was about 9%). There has not been any new SARS case reported since 2004 [2,10,11].…”

Section: Introductionmentioning

confidence: 99%

Laboratory detection methods for the human coronaviruses

Shabani

Dowlatshahi

Abdekhodaie

2020

Eur J Clin Microbiol Infect Dis

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Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection methods were classified and presented in this article. The laboratory detection techniques include RT-PCR, RT-LAMP, electrochemical and optical biosensors for RNA detection, and whole virus or viral proteins detection assays.

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Coronaviruses

Cited by 128 publications

References 5 publications

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting

Laboratory detection methods for the human coronaviruses

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