Question

1. The “novel coronavirus” (SARS-CoV-2) that is causing much concern this winter/spring is a member of the family Coronaviridae.  Describe the structure, and the nature of the genetic material, of the Coronaviridae.  

Answer 1

The coronoaviridiae are family of viruses of the order Nidovirales. They are a group of viruses that contain non-segmented positive sense RNA genome surrounded by an envelope.

Virus Structure: These are spherical viruses with a diameter of 125 nm. The envelope has club like spikes, giving a structure like corona. Within the envelope, lies the helical and symmetrical nucleocapsid enclosing the RNA genome. There are four main structural proteins- Spike (S), membrane (M, envelope (E) and nucleocapsid (N) proteins. The spike S protein is a heavily glycosylated protein that has N-linked glycosylation. The spike proteins as present as homotrimers forming the spike structures of the envelope. This S glycoprotein is involved in attachment to the receptor on host cells/ S can be cleaved to S1 (receptor binding domain) and S2 (spike stalk) by furin like proteases.

The Membrane M proteins have 3 transmembrane domain that form the shape of virus. The M protein has two regions- N terminal ectodomain that is glycosylated and C-terminal endodomain. The E protein is mostly a transmembrane protein with N –terminal Ectodomain and C-terminal endodomains. This protein has ion channel activity that has relevance in pathogenesis. This E protein is mostly involved in assembly and release of virus. N proteins are present in nucleocapsid and have the RNA binding Ectodomain and endodomains. The N protein is phosphorylated and can bind to nsp3 that forms the replicase complex. Apart from these structural proteins, some coronaviruses also encodes a hemagglutinin-esterase (HE), which can bind sialic acid residues. This HE has acetyl esterase activity that helps in S protein mediated entry into mucosal cells.

RNA Genome Nature: The viral genome is quite large, and is approximately 30 Kb in size. The RNA has a 5’ CAP and a 3’ poly A tail. Both the 5’ and 3’ end have untranslated regions. The 3’ poly A tail allows the RNA to be used as mRNA. This mRNA is then translated to form replicase polyproteins. Replicase polyproteins are translated from replicase gene that is around 20 Kb in size. These polyproteins are nonessential proteins. The rest of the 10 kb genome codes for structural and accessory proteins.

At the 5’ end, the RNA genome has a leader sequence and untranslated region (UTR). Several stem loop structures are present in the UTR. These structures are essential for transcription and replication of RNA genome. The structural genes include the spike, envelope, membrane and nucleocapsid genes. Each structural or accessory gene also has regulatory sequences called TRSs (transcriptional regulatory sequences). These TRSs regulate expression of these genes. At the 3’ end, RNA structures are present in the untranslated region (3’ UTR) that is involved in replication or synthesis of the RNA of virus.