Packaging the Corona Genome

Genome packaging intro

Review (pmid: 31505321)

• there is conflicting evidence as to whether the viral nucleocapsid protein or the membrane protein plays the primary role in packaging signal recognition.
• The most fundamental formulation of the packaging problem is: how do viruses ensure the specific incorporation of their genomes into assembled virions, faced with competition from numerous other nucleic acid species in the infected cell? A broad array of positive-strand RNA viruses (picornaviruses, flaviviruses, alphaviruses, coronaviruses, and retroviruses) and negative-strand RNA viruses (rhabdoviruses, paramyxoviruses, and orthomyxoviruses) are generally held to selectively package genome-length RNA of the correct polarity and to exclude other viral and host species.
• Specific packaging is often mediated by well-defined cis-acting RNA sequences or structures within the viral genome, designated packaging signals (PSs). One of the most intensively studied PS elements, named psi, - 5′ leader region of the HIV genome. The mechanism by which - studies have revealed that genome dimerization promotes the folding of psi and neighboring RNA elements into a conformer in which the genomic splice donor site is sequestered (Keane et al., 2015, 2016).
• the genomes of coronaviruses are nonsegmented, positive-sense RNA molecules of exceptional length (25–32 kb), with 5′ caps and 3′ polyadenylate tails
• viral infection entails not only replication of gRNA but also production of a set of subgenomic (sg) RNAs that serve as mRNAs for the downstream genes. The sgRNAs, synthesized via negative-strand intermediates, form a nested set, each member of which contains a 5′ genomic leader RNA fused to a segment of the 3′ end of the genome
• the assembly of the nucleocapsid into the virion occurs through interactions between the carboxy termini of multiple monomers of N protein and of M protein (Escors et al., 2001; Hurst et al., 2005; Verma et al., 2006).
• For coronaviruses, the packaging problem amounts to achieving highly specific recognition and selection of gRNA from among an abundance of viral sgRNAs, cellular mRNAs, and other RNA species in infected cells. - stringently purified virions almost exclusively contain positive-sense gRNA (Makino et al., 1990; Escors et al., 2003; Kuo and Masters, 2013). In the relatively few cases where it has been examined in detail, this selectivity has been found to be accomplished by means of a genomic PS.

The packaging signal PS

(pmid: 31505321) PSs of coronaviruses are not broadly conserved across the family. Coronaviruses are taxonomically classified into four genera alpha, beta, gamma, and deltacoronaviruses – and these are further sorted into lineages or subgenera. In particular, the betacoronaviruses comprise four phylogenetic lineages. The first of these, the lineage A betacoronaviruses, provided the foundation for coronavirus packaging studies and, so far, have remained their principal focus.

(2010 pmid: 20202661) It has been generally found that a strong PS or encapsidation signal, usually encompasses repetitions of conserved (structural) motifs (Hellendoorn et al., 1996, Chen et al., 2007). This leads us to propose that the SL5 substructures bearing the highly conserved UUYCGU repeats function as genomic PS for group I and II CoVs, including SARS-CoV.

How is the RNA organized within the virus

Double membrane vesicles - DMV

Betacoronavirus lineage A packaging signals (MHV-PS)

Betacoronavirus lineage B (SARS-CoV)

PS of Betacoronavirus lineage B (ie SARS-CoV)

two possible locations:

5' PS

predicted RNA structures of the genomic 5′ ends of all coronaviruses (Chen and Olsthoorn, 2010).

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