Genes of eleven coronaviruses from the four genera — coronavirus

The genes of eleven coronaviruses, the genomes of Fig. 1 of the reference: HCoV-229E and HCoV-NL63 (Alphacoronavirus), MHV, HCoV-OC43, HCoV-HKU1, MERS-CoV, SARS-CoV-1, SARS-CoV-2 and the bat coronavirus RaTG13 (Betacoronavirus), IBV (Gammacoronavirus) and PDCoV (Deltacoronavirus). They are in that order, by genus and subgenus, so that each genome sits next to its closest relatives here. Made by data-raw/coronavirus_genomes.R.

Usage

coronavirus_genomes

Format

A data frame with 148 rows and 15 columns:

cluster: Short name of the virus, e.g. "SARS-CoV-2". A character vector.
genus: Genus of the virus, e.g. "Betacoronavirus". A character vector.
subgenus: Subgenus of the virus, e.g. "Sarbecovirus". A character vector.
virus: Name of the virus. A character vector.
strain: Strain or isolate, as in the record. A character vector.
host: Host of the virus, e.g. "human" or "bat". A character vector.
accession: GenBank or RefSeq accession of the genome. A character vector.
gene: Gene name, e.g. "ORF1a", "S", "3a" or "9b", or "L" and "3'UTR" for the untranslated ends. A character vector.
product: Description of the gene product, from the record. A character vector.
category: Role of the gene: "5' UTR", "ORF1a", "ORF1b", "spike", "hemagglutinin-esterase", "envelope", "membrane", "nucleocapsid", "accessory" or "3' UTR". A character vector.
start: Start position of the gene in the genome. A numeric vector.
end: End position of the gene in the genome. A numeric vector.
strand: Strand of the gene; all are "forward". A character vector.
homolog: Chain of homologous genes across neighbouring genomes of the same genus, named after its first gene, e.g. "MHV 5a" for 5a of MHV, ns12.9 of HCoV-OC43 and 4 of HCoV-HKU1, for GC_links()(group = "homolog"); NA for a gene without a homolog next to it. A character vector.
identity: Protein identity, in percent, of the gene to its homolog in the genome above; NA for the first gene of a chain. A numeric vector.

Source

GenBank accessions AF304460, AY567487, AY903460, AY597011, MN996532 and AY274119 and RefSeq accessions AC_000192, NC_019843, NC_045512, NC_001451 and NC_039208, read with read_gbk().

Details

The genes are read from the GenBank records and named as in the literature, e.g. "3a" for the "Orf3" of SARS-CoV-1 and the "NS3" of RaTG13. ORF1ab is split at its -1 ribosomal frameshift into ORF1a and ORF1b. Fourteen accessory ORFs that the records do not annotate are added from their position in the genome (product ends in "(not annotated in the record)"): the ORFs that lie inside N in another reading frame (Ia and Ib of HCoV-229E and HCoV-NL63, 9b and 9c of RaTG13 and SARS-CoV-2, 8c of MERS-CoV), 3b, 3c and 3d inside ORF3a of SARS-CoV-2 and 3b of RaTG13 (the SARS-CoV-2 ORFs are described by Jungreis et al., 2021), and ORF10 of RaTG13, which matches ORF10 of SARS-CoV-2. Each runs from an ATG to its first stop codon. MHV is strain JHM, as the records of strain A59 leave out HE, 4 and 5a.

Homologous genes of closely related neighbouring genomes share a homolog. Every gene is translated from the genome and aligned to the genes of the next genome with protein_blast(). Only neighbours whose ORF1b, which holds the polymerase and is the most conserved protein, is at least 70% identical are joined: the genomes of a subgenus and the two alphacoronaviruses (82%), but not the subgenera of the betacoronaviruses (62-66%) or the genera (50-56%), whose proteins are so far apart that their identity says little. The cut-off is chosen for these genomes, not an official one. Between close relatives, the core genes (ORF1a, ORF1b, S, HE, E, M and N) are homologous and are joined to the same gene of the next genome, however low their identity. Accessory genes are joined when each is the other's best hit, with at least 30% identity, or 50% when either protein is shorter than 50 amino acids, as short alignments reach a third identity by chance.

Each genome also has a row for its 5' untranslated region, named "L" after the leader sequence it starts with, from the start of the genome to ORF1a, and one for its 3' untranslated region ("3'UTR"), from the last gene to the end of the genome.

References

Chazal N. Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes? Front Microbiol. 2021;12:682603.

Jungreis I, Sealfon R, Kellis M. SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes. Nat Commun. 2021;12:2642.

Examples

GC_chart(coronavirus_genomes, cluster = "cluster", group = "category",
         height = "700px") %>%
  GC_labels("gene") %>%
  GC_clusterLabel() %>%
  GC_zoom(range = c(0.75, 1))