Lecture 3 Genome and Viral Replication

How many viruses affect humans?

250 to 300 viruses affect humans, and overall, there may be around 10 million species of viruses on Earth, leading to a vast number of potential viral species that remain largely unknown.

Which is more stable RNA or DNA and why?

RNA is more susceptible to degradation than DNA, which contains a deoxyribose, giving it structural stability.

How many proteins can RNA viruses on average produce compared to humans?

about 10 - 40 proteins compared to humans, who average about 22 000 proteins. Each type of virus has specific proteins necessary for its replication and pathogenicity.

What are viroids and virusoids

They are RNA entities consisting of small circular RNA strands that can cause disease leading to crop failures, although they do not kill the plants outright.

Which is bigger DNA or RNA viruses and why?

This inherent strength contributes to a broader size range of DNA viruses, which can range from 5 to 350 kilobases, whereas RNA viruses usually vary from 5 to 40 kb, with 40 kb being the maximum size for a virus like coronavirus.

The inherent strength of DNA viruses contributes to its broader size of 5 - 350 kb. Compared to RNA which vary from 5 - 40 kb.

max size for viruses like coronavirus is 40 kb

What are some general properties of viral genomes

Linear, circular, single stranded, double stranded structures and whether they are positive or negative sense.

How are RNA viruses classed?

based on their genome types

What are some RNA groups that are classified based on their genome types

• positive sense RNA virus - their genomes can serve directly as mRNA

• negative sense RNA viruses - their genomes must be converted to a positive sense mRNA by RNA dependent RNA polymerase (RdRPs) prior to translation. 

• double stranded RNA viruses. - these require specific mechanisms for replication, seen notably with rotaviruses. 

What are some specific polymerases that viruses use for genome replication and to synthesize proteins?

• RdRP RNA dependent RNA polymerase - for RNA viruses

• DNA dependent DNA polymerase for DNA viruses

What is the process of initiating genome replication for RNA viruses

RNA viruses can function through de novo mechanisms or utilize primers, including RNA primers similar to those found in bacterial systems. 

What is the process of initiating genome replication for DNA viruses

DNA viruses typically replicate within the host nucleus and follow a more straightforward transcription and translation process. 

zika virus

• a flavivirus, positive sense RNA

• causes fever, rash, join pain, red eyes

• also causes congenital disabilities (related to birth and pregnancy) like microcephaly (brain impairment in birth)

Hepatitis C

• flavivirus, positive sense RNA

• major cause of liver disease

Norovirus

• a calicivirus, positive sense RNA

• common cause of gastroenteritis 

Coronavirus

• a large positive sense RNA virus

• Responsible for respiratory diseases like COVID 19

what is the RNA world hypothesis

• where RNA molecules stored genetic information and catalysed biochemical reactions before the evolution of DNA and proteins

How many proteins can RNA viruses code?

• Coronavirus can code 28 proteins many of which are polyproteins that are later cleaved

• Hep C and Norovirus code for about 10 proteins. These proteins include structural components, replication machinery and immune evasion factors

How can DNA genomes encode for more proteins than RNA genomes?

Due to their larger genome size and more stable nature, allowing the to carry more complex genetic information and often replicate in the host nucleus. 

what are some examples of positive sense RNA viruses

coronavirus and hep c which can directly serve as mRNA

what are some examples of negative sense RNA viruses

influenza, rabies which must first be transcribed into positive sense RNA by RDRP.

How do DNA viruses replicate?

They replicate similarly to plasmids, often involving the host cell nucleus for transcription and DNA replication. They utilise host DNA polymerases or their own encoded polymerases. 

How do bacteriophages replicate?

Viruses that infect bacteria. They exhibit similar replication strategies as DNA viruses, but are distinct in their structure (often complex with a head and tail morphology) and mechanism of infection (injecting their genome into the bacterial cell). 

How do RNA viruses replicate

primarily need RNA dependent RNA polymerase (RDRP) for replication and transcription as host cells lack this enzyme. Replication occurs in the cytoplasm and involves a double stranded RNA intermediate.

what type of structure do Bacteriophages (e.g T4 phage) and Poxviruses (Vaccinia virus) have

They possess intricate structures that do not conform to simple helical or icosahedral symmetry. 

Poxviruses - have a dumb bell shaped core and replicate entirely in the cytoplasm

what type of structure do Helical and Icosahedral viruses have

They have variations in structural formation affecting infection processes and immune evasion. 

helical capsids (e.g tobacco mosaic virus, rabies virus) are rod shaped, with protomers arranged helically around a central axis.

icosahedral capsids (e.g adenovirus, herpesvirus) are roughly spherical, composed of 20 triangular faces, providing a robust and efficient way to enclose the genome. 

What diseases is papillomavirus used to treat

Used in cervical cancer prevention, creating a HPV vaccine that targets specific strains.

What disease is Adenovirus used to treat?

Causes Common cold, conjunctivitis and often used in gene therapy vectors

What disease is herpes virus used to treat?

Large DNA viruses. It causes congenital infections, cold sores (HSV - 1), genital herpes (HSV - 2), chicken pox/shingles (VZV), and various other diseases (CMV, EBV).