Coronavirus Genome Structure and Replication

By D. Brian, Ralph S. Baric. Current Topics in Microbiology and Immunology, 2005

703 citations recorded by the source corpus.

In addition to the SARS coronavirus (treated separately elsewhere in this volume), the complete genome sequences of six species in the coronavirus genus of the coronavirus family [avian infectious bronchitis virus-Beaudette strain (IBV-Beaudette), bovine coronavirus-ENT strain (BCoV-ENT), human coronavirus-229E strain (HCoV-229E), murine hepatitis virus-A59 strain (MHV-A59), porcine transmissible gastroenteritis-Purdue 115 strain (TGEV-Purdue 115), and porcine epidemic diarrhea virus-CV777 strain (PEDV-CV777)] have now been reported. Their lengths range from 27,317 nt for HCoV-229E to 31,357 nt for the murine hepatitis virus-A59, establishing the coronavirus genome as the largest known among RNA viruses. The basic organization of the coronavirus genome is shared with other members of the Nidovirus order (the torovirus genus, also in the family Coronaviridae, and members of the family Arteriviridae) in that the nonstructural proteins involved in proteolytic processing, genome replication, and subgenomic mRNA synthesis (transcription) (an estimated 14–16 end products for coronaviruses) are encoded within the 5′-proximal two-thirds of the genome on gene 1 and the (mostly) structural proteins are encoded within the 3′-proximal one-third of the genome (8–9 genes for coronaviruses). Genes for the major structural proteins in all coronaviruses occur in the 5′ to 3′ order as S, E, M, and N. The precise strategy used by coronaviruses for genome replication is not yet known, but many features have been established. This chapter focuses on some of the known features and presents some current questions regarding genome replication strategy, the cis-acting elements necessary for genome replication [as inferred from defective interfering (DI) RNA molecules], the minimum sequence requirements for autonomous replication of an RNA replicon, and the importance of gene order in genome replication.

Subfields: Animal Science and Zoology, Infectious Diseases

View Paper: https://www.semanticscholar.org/paper/9afed70c82fe4ae19b1dc2f70bb3daf3b0aeea36

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Citations in the corpus

Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein (2017, background): “The 5′-terminal two thirds of the genome include two open reading frames (ORFs), 1a and 1b, that together encode all non-structural proteins for the formation of the RTC, whereas the 3′proximal third encodes the structural and accessory proteins (Fig. 1A; Brian and Baric, 2005).”
Discovery of Seven Novel Mammalian and Avian Coronaviruses in the Genus Deltacoronavirus Supports Bat Coronaviruses as the Gene Source of Alphacoronavirus and Betacoronavirus and Avian Coronaviruses as the Gene Source of Gammacoronavirus and Deltacoronavirus (2012, background): “Based on genotypic and serological characterization, CoVs were traditionally divided into three distinct groups (3, 22, 54).”
Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination (2011, background): “Based on genotypic and serological characterization, coronaviruses traditionally were classified into three distinct groups, groups 1, 2, and 3 (4).”
Coronavirus Pathogenesis and the Emerging Pathogen Severe Acute Respiratory Syndrome Coronavirus (2005, background): “frameshift mechanism, which occurs at high frequency (25 to 30%) (25, 27).”
SARS-CoV-2: Structure, Biology, and Structure-Based Therapeutics Development (2020, background): “The nucleocapsid protein (N) formed the capsid outside the genome and the genome is further packed by an envelope which is associated with three structural proteins: membrane protein (M), spike protein (S), and envelope protein (E) (Brian and Baric, 2005).”
Molecular diversity of coronaviruses in bats (2006, background): “Based on genotypic and serological characterization, coronaviruses were divided into three distinct groups (Lai and Cavanagh, 1997; Ziebuhr, 2004; Brian and Baric, 2005).”
First infection by all four non-severe acute respiratory syndrome human coronaviruses takes place during childhood (2013, background): “; licensee BioMed Central L Commons Attribution License (http://creativec reproduction in any medium, provided the or Coronaviruses are phenotypically and genotypically diverse [6,10].”
Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System? (2019, background): “These ubiquitous human pathogens are molecularly related in structure and mode of replication with neuroinvasive animal coronaviruses [176] like PHEV (porcine hemagglutinating encephalitis virus) [177] , FCoV (feline coronavirus) [178, 179] and the MHV (mouse hepatitis virus) strains of MuCoV [180] ”
The SARS-Coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds (2014, neutral): “Coronavirus (CoV) replication is a highly orchestrated process involving complex replication machineries to protect the virus genome, the largest known RNA genome, and the viral proteins from the host’s antiviral defense mechanisms (Brian and Baric, 2005).”
The Molecular Biology of Coronaviruses (2006, background): “However, although some heptanucleotides showed a frameshifting efficiency nearly as high as that of the wild type, it must be noted that, to date, all known coronaviruses have been found to contain a slippery sequence of UUUAAAC (Brian and Baric, 2005; Plant et al., 2005).”