Question

Describe the SARS-CoVid-2  virus replication cycle, describe the attachment molecules, mechanism of penetration and uncoating, where the genome is replicated and how the virus exits the cell.

Answer 1

SARS-CoV-2 virus, commonly known as COVID19 belongs to the coronavirus family. It was originally found in bays, but has now mutated and infected humans. It shares 79.5% homology with SARS-CoV virus. It is an enveloped RNA virus that has spikes on its envelope. Incubation period is around 1-14 days with a mean of 5 days. Ro ranges from 2.2-3.58 for the virus. The capsid is made up of spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. The genome is positive sense single stranded RNA of around 28-32 Kb.

The virus infects the nasopharyngeal cells when inhaled as droplets from infected person. Attachment to nasopharyngeal cells is by the Spike S protein present on the envelope of the virus. The S protein is made up of two domains- S1 and S2 domain. The S1 domain contains the receptor binding site while the S2 domain causes fusion with cell membrane. The S1 domain binds to the ACE2 receptors (angiotensin converting enzyme 2) on target cells. The receptor binding domain in S1 has a core region and an external subdomain. The binding of S1 domain of SARS-Cov-2 to ACE2 is nearly 10-20% higher than binding of SARS-CoV to ACE2. The S2 domain will then mediate membrane fusion. The membrane of virus capsid and the host cell membrane will fuse and the ssRNA is introduced in the cytosol. Transmembrane protease serine 2 (TMPRSS2), furin and cathepsins are molecules that are involved in membrane fusion. Receptor mediated endocytosis by clathrin mediated method is also proposed as a mechanism for entry of viral genome. In this case, cathepsin L1 has been proposed to activate the spike protein. The ssRNA is then uncoated and will enter the cytoplasm.

Polyproteins are then translated from viral genome. The viral proteinases such as Papain-like protease (Pl pro ) and 3C-like protease(3CL pro ) will cleave polyprotein pp1a and pp1ab. This cleavage results in production of functional nonstructural proteins (NSPs). These NSPs include helicases or RNA replicase–transcriptase complex (RCT).

RCT is involved in formation of the anti-sense negative RNA strand form the positive sense genomic RNA. The RdRp will produce the antisense negative strand RNA, which is complementary to mRNA. This full length negative strand is processed to produce shorter subgenomic negative sense RNAs. These short negative sense RNAs are translated to structural proteins S, E, M and N. They are also use to form non-structural accessory proteins.

The negative strand RNA, also acts as a template for positive strand synthesis during the viral genomic RNA replication. The negative strand RNA is then converted to plus-strand RNA by RCT complex. The structural proteins S1, S2, M and E are transcribed on ribosomes bound to the Endoplasmic reticulum. The nucleocapsid N proteins are translated in the cytoplasm.

The plus strand viral RNA produced after replication will be transported to the assembly sites along with structural and non-structural protein. This assembly site is between ER and Golgi. In the assembly sites, the virions are assembled. They will enter the Golgi, undergo further processing and then bud off as small vesicles. The small vesicles will migrate to the cell membrane where they will fuse with the cell membrane. This releases the virions into the extracellular space. Such a type of lysis is known as non-lytic exocytosis. Thus, the new virions are no ready to infect next host cells.