31st July 2023

Clinical Virology

Pathophysiology

The full scope of virus pathophysiology is beyond the remit of this section. Key principles to remember include:

• Viruses rely on a host to replicate and propagate
• Many of the clinical manifestations are the result of the immune response triggered by viral replication
• Host cell lysis will result in cell death locally and also contributes to the clinical illness

Viruses often have a specific action on a particular body system, owing to their individual molecular characteristics – this is known as tropism. Some viruses can cause disease in multiple tissue types, e.g. cytomegalovirus (CMV) in the immunosuppressed individual, which can cause CMV colitis, encephalitis, retinitis and hepatitis.

Assessment and diagnosis

Diagnosis in modern medicine relies predominantly on nucleic acid-based methods and serological assays. However, microscopy-based methods such as immunofluorescence with electron microscopy are also still used.

Samples can be taken from a range of sites specific to the virus in question. For example, if viral encephalitis is suspected, a lumbar puncture is the best method to obtain a sample.

Polymerase chain reaction (PCR)

PCR is a method by which viral DNA can be replicated in order to be detected. Molecular probes known as ‘primers’ are designed that are specific to a certain virus genome. The polymerase enzyme, and heat, are then used to create a reaction in which if any viral DNA is present in the sample tested, it will replicate and be amplified to detectable levels, making the test ‘positive’.

Reverse transcription PCR (RT-PCR) is the same principle but for the detection and amplification of RNA.

Sequencing

Genetic sequencing uses the product amplified from PCR/RT-PCR and is analysed by a sequencing machine. It enables the full sequence of a viral genome to be analysed.

Immunofluorescence

This technique makes use of an antibody specific to the virus suspected in a sample of potentially infected tissue. A chemical, or specific wavelength of light, is applied to the tissue sample. This enables visualisation of the antibody, and hence the virus, if present.

Electron microscopy

Electron microscopy was the traditional mainstay of virology. However, modern techniques require less technical skill and are quicker, so they have overtaken it. The advantage is that through electron microscopy, you can visualise a whole virus, revealing its shape and structure (see image below), and it is useful if viruses do not show up on routine diagnostic tests or if suspicious results need interrogating further.

Electron micrograph of Ebola virus

Image Source: Wikimedia Commons (2011). Ebola virus virion, Licensed under a creative commons licence. Available for free at: https://commons.wikimedia.org/wiki/File:Ebola_virus_virion.jpg (Accessed: 19 September 2022).

When Ebola was first discovered in 1976, it was electron microscopy of the virion that showed it had a different structure to the yellow fever virus, which was initially thought (wrongly) to be the cause of the outbreak in the Democratic Republic of Congo.

Serology

Serological diagnosis is performed through the detection of antibodies and antigens from patient blood samples. IgM antibodies indicate an acute infection. IgG antibodies indicate prior exposure, and hence either vaccination or previous infection.

Antiviral drugs and vaccines

Antivirals

There are relatively few antivirals available in comparison to antibiotics. One of the most common antivirals prescribed in clinical medicine is aciclovir – which is effective against herpes simplex virus and varicella zoster virus (the cause of shingles). Aciclovir and the related agents famciclovir and valaciclovir work through being phosphorylated by viral tyrosine kinase, resulting in early chain termination.

Antiretrovirals

HIV antiretroviral medications are numerous. HIV treatment is based on the principle of utilising multiple methods of attack on the virus simultaneously, known as highly active antiretroviral therapy (HAART). These drugs have revolutionised HIV treatment, making it a manageable, chronic illness. More information can be found in the HIV and Infections in Immunocompromised Hosts topic.

Vaccines

Multiple viruses now have effective vaccines against them. These vaccines can be classified by type. Classical types include live attenuated, toxoid, conjugate, and inactivated vaccines. More recent times have seen the advent of mRNA vaccines, which use the host’s genome to build the proteins that then mount a humoral immune response. Many of the new vaccines against COVID-19 are mRNA vaccines.

Some common vaccines are summarised by type in the table below.

Table 1: Examples of viral vaccines by type

Live attenuated vaccines should be avoided in the immunosuppressed. A full UK vaccine schedule can be found on the NHS website and is linked in the References section here.

Influenza antivirals and vaccines

The 2009 swine flu pandemic, caused by the H1N1 influenza virus, led to a rise in the use of oseltamivir (Tamiflu) and, less so, zanamivir (Relenza). These drugs are neuraminidase inhibitors, which block the binding of the neuraminidase antigen of the influenza virus to sialic acid receptors in the lung.

However, there is little evidence that oseltamivir prevents the complications of influenza; although it can help people recover from the illness more quickly. The evidence base for zanamivir is also weak, but it is regularly used to treat influenza A and B infections.

Influenza vaccines are adjusted each year, depending on the seasonal variants that have become dominant worldwide, which is why viral surveillance is so important. Influenza A and influenza B are the most common strains of the virus, and the vaccine is based around these. Most influenza vaccines contain traces of eggs, which is important to know for allergy purposes.