Compare the replication cycles of an orthomyxovirus and a coronavirus 3 PDF

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Compare the replication cycles of an Orthomyxovirus (flu) and Coronavirus Coronaviruses e.g. SARS +ssRNA -

S protein, S1 binds to cell receptor and S2 causes membrane fusion to enter the cell o Genome is capped and tailed

Replication: -

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Frame shift mechanisms (ORF1a and b) o Due to slippery sequence in the region of overlap between the ORFs and a pseudoknot structure Polyprotein processing Makes antigenome from which genome is made Also makes nested set of mRNAs o From original genome and becomes anti-mRNA (all have same 3’ tail and 5’cap) o 1st ORF of each set usually read o Nested RNAs depend of TRS sequence which determines amount made

Assembly: -

N protein and full length genome assemble in cytoplasm Interacts with M protein and buds into intracellular ER membranes Vescile fusion with plasma membrane to release mature particle

Orthomyxovirus Entry: -

HA binds to sialic acid on cell surface

Replication: -

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Occurs in nucleus Cap stealing Full length antigenome synthesis 8 segments of –ssRNA Also able to make multiple proteins from 1 nucleotide sequence: o Splicing (as it is in nucleus) o Start stop cistrons – overllaping Stop and Start sequence so it may reinitiate o Leaky scanning Post translational cleavage

Assembly

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In cytoplasm – targeted to apical plasma membrane M1 causes membrane bending which leads to budding

Orthomyxoviruses and Coronaviruses share some similarities but also some differences in regards to their replication cycles. The Orthomyxovirus, Influenza, and the coronavirus, SARS coronavirus (SARSCoV), will be used for examples of similarities and differences. Firstly, Influenza is an enveloped segmented negative-sense single stranded RNA virus. SARS-CoV on the other hand is an enveloped positive-sense single stranded RNA virus. The entry and fusion of the viruses are similar in the way that they both require specific cell receptors to enter the host cell. Influenza has haemagluttinin (HA) trimeric protein which binds to sialic acid on the host cell surface. HA has 2 domains, HA1 which is responsible for receptor binding and HA2 for the fusion of the membranes. SARS-CoV has a Spike (S) protein that binds to angiotensin-converting enzyme 2 (ACE-2). S protein is similar as it is a trimer and has 2 domains as well; S1 which is responsible for receptor binding and S2 to cause membrane fusion. Although similar in function and structure, HA is a class 1 fusion protein, while S protein is not. S protein just shares similarities however cleavage is not essential for coronavirus infection. The replication stage of their cell cycles is probably what varies the most. SARS-CoV replicates its viral genome within the cytoplasm while Influenza replicates within the nucleus, which gives rise to a few different methods for transcription and translation. SARS-CoV genome has a 5’ cap and a 3’ poly-A-tail. It maximises its genome through a variety of mechanisms such as a frame-shift. When transcribing from the genome, there can occasionally be a frame-shift from ORF1a to ORF1b due to a slippery sequence, UUUAAAC, in the region of overlap between the ORFs. There is also a 3D pseudoknot structure which contributes to this and allows a longer polypeptide to be created. Another mechanism it uses is polyprotein processing. It employs the use of its own proteases to produce smaller proteins such as mature replicase proteins. A mechanism it uses that Influenza does not, is the use of nested mRNAs. It is a group of mRNAs from the original genome that have the same 3’ poly-A-tail and 5’ cap. Usually only the 1 st ORF is read from each nested mRNA and different amounts of the different proteins are made. As influenza virus is a negative sense virus, it must carry its own copy of RdRp. It has a ribonucleoprotein (RNP) complex that includes this. Influenza genome is not capped and therefore requires a way to cap its genome in order to allow translation of its proteins. This is solved by the mechanism of cap stealing. Protein PB2, a component of the RNP complex, binds to the capped 5’ end of newly synthesised host cell mRNAs, and cleaves 10-13 bases including the cap. This segment of RNA is then used as primer for influenza mRNA synthesis. PB1 and PA, also part of the RNP complex, initiates transcription and extends the primer. As it replicates in the nucleus, it has the access to host cell machinery for splicing. Splicing allows multiple proteins to be made from the same strand of RNA. Segment 7 of Influenza A encodes for M1 protein however is also able to make M2 due to splicing mechanisms. It also uses start-stop cistrons. When RdRp is reading down the frame, it may read AUG (a start codon) instead of UAA (a stop codon) as it is overlapping each other and leads to reinitiation of synthesis. Leaky scanning is also another mechanism used where it may miss and start at an alternate start codon in a different frame resulting in different proteins....