The strategy of expression of the coronavirus genome is unique. The infectious, plus sense viral RNA is translated directly, the product of the
5' two-thirds of the genome being two polyproteins, the larger of which is
produced by ribosomal frame-shifting; each is post translationally self-cleaved
and the resulting polypeptides assembled to form an RNA polymerase. This
enzyme is then employed to transcribe a full-length complementary (minus
sense) RNA, from which in turn are transcribed not only full-length new plus
strands, but also a 3'-coterminal nested set of sub genomic RNAs. The nested set
comprises 5-7 overlapping species of plus sense mRNAs which extend for
different lengths from their common 3' ends and share a common 70 nucleotide
5' leader sequence.
They are generated by a leader-primed mechanism
of discontinuous transcription, whereby the polymerase first transcribes the
noncoding leader sequence from the 3' end of the minus sense anti genome,
then the capped leader RNA dissociates from the template and re associates
with a complementary sequence at the start of any one of the genes to continue
copying the template right through to its 5' end. Only the unique sequence
toward the 5' end which is not shared with the next smallest mRNA in the
nested set is translated, the product therefore being a unique protein in most
cases. A puzzling finding is that sub genomic minus sense RNA species complementary to the nested set of plus sense mRNAs are also present in infected
cells, giving rise to the intriguing possibility that coronavirus mRNAs may be
self-replica ting.
The synthesis, processing, oligomerization, and transport of the several
envelope glycoproteins have been studied in depth and dispIay some unusual
features. For example, the envelope protein M, which in some coronavirus species contains 0-linked rather than N-linked glycans, is directed exclusively to certain internal membranes, namely, cisternae of the endoplasmic reticulum and the Golgi complex, as a result of which virions bud only from
these regions and not from the plasma membrane. The virions are then transported
in vesicles to the plasma membrane for exit From the cell by exocytosis.
Following their release many of the mature enveloped virions
remain adherent to the outside of the cell. The whole of the replication cycle is
confined to the cytoplasm, and indeed can occur in enucleate cells.
Genetic recombination occurs at high frequency between the gemmes of
different but related coronaviruses, This may be an important mechanism for
generation of genetic diversity in nature.
Coronavirus genomes contain 5 and 3UTRs ranging in size from 200 to 600 and from 200 to 500 nt, respectively. Signals for genome replication and encapsidation reside not only in these UTRs, but also in adjacent and more internal coding regions. Six ORFs are conserved subfamily-wide and
arranged in a fixed order: (as listed in the 5 to-3 direction) ORFs 1a and 1b, together comprising the replicase gene, and the ORFs for the structural proteins S, E, M and N. Downstream of ORF1b and interspersed between the structural protein genes, there may be up to at least eight accessory
(also called “group” or “niche-specific”) genes, the products of which are generally dispensable for replication in vitro, but key to efficient replication during natural infection.