Question

1. What proteins are encoded in the SARS-CoV-2 genome? What is the general function of each?

Answer 1

A new disease, termed severe acute respiratory syndrome (SARS), emerged at the end of 2002 and caused profound disturbances in over 30 countries worldwide in 2003. A novel coronavirus was identified as the aetiological agent of SARS and the 30 kb viral genome was deciphered with unprecedented speed in a coordinated manner by the global community.

Since then, much progress has been made in the virological and molecular characterization of the proteins encoded by SARS-coronavirus (SARS-CoV) genome. The SARS-coronavirus (SARS-CoV) genome is ∼30 kb in length and contains 14 potential open reading frames (ORFs)

These investigations can be broadly classified into three groups:

(a) studies on the replicase 1a/1b gene productsw which are important for viral replication,

(b) studies on the structural proteins, spike, nucleocapsid, membrane and envelope, which have homologues in all coronaviruses, and are important for viral assembly and

(c) expression and functional studies of the “accessory” proteins that are specifically encoded by SARS-CoV.

Replicase gene (ORFs 1a and 1b)

The first 2/3 of the SARS-CoV genome encodes the viral replicase genes (ORFs 1a and 1b), which translates into two large polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Expression of the ORF 1b-encoded region of pp1ab involves ribosomal frameshifting into the −1 frame just upstream of the ORF 1a translation termination codon.

Proteolytic processings of these polyproteins are mediated by viral cysteine proteinases and produces a minimum of 13 non-structural proteins (also called nsp's), some of which are responsible for replicating the viral genome and/or generating a nested set of subgenomic mRNAs to express all the ORFs downstream of ORF 1b.

Strucural proteins (S, E, M and N)

Coronaviruses are positive-strand RNA viruses and the virion consists of a nucleocapsid core surrounded by an envelope containing three membrane proteins, spike (S), membrane (M) and envelope (E) that are common to all members of the genus (Siddell, 1995, Lai and Holmes, 2001).

The RNA is packaged by the nucleocapsid (N) protein into a helical nucleocapsid.

The S protein, which forms morphologically characteristic projections on the virion surface, mediates binding to host receptors and membrane fusion.

The M protein is a triple-spanning integral membrane protein with a short ectodomain and a large carboxyl-terminus endodomain.

More recently, the E protein was shown to play a major role in coronavirus assembly

Accessory proteins

Group-specific genes in coronaviruses, also called “accessory” proteins, are usually dispensable for viral replication in cell culture systems but may be important for viral–host interactions and thus contribute to viral stability and/or pathogenesis in vivo.

These accessory proteins vary in size and position in the genome.

Eight subgenomic mRNAs are produced in SARS-CoV infected Vero E6 cells and these are used to express the ORFs besides the replicase 1a/1b. These include the S (ORF 2), E (ORF 4), M (ORF 5) and N (ORF 9) and another eight ORFs that encode putative proteins with no significance sequence homology to viral proteins of other coronaviruses (ORF 3a, 3b, 6, 7a, 7b, 8a, 8b and 9b).

Of these SARS-CoV-unique ORFs, two of them (3a and 7a) have been shown to be expressed during SARS-CoV infection (Fielding et al., 2004, Tan et al., 2004c, Yu et al., 2004, Zeng et al., 2004b) and antibodies against another four of them (3b, 7b, 8a and 9b which were termed as ORF 4, 9, 10 and 13, respectively, in Guo et al., 2004) have been detected in the sera of convalescent patients, suggesting that these proteins were expressed during infection in vivo.