SARS-COVID-2 and the respiratory system

A quick understanding of the damages and symptomatic treatments

This chapter is a follow-up on the Chapter 43 Gaz exchanges in animals centred around the recent outbreak of the COVID-19 pandemic.


The new coronavirus, also known as COVID-19 was discovered in late 2019 in Wuhan, China when numerous cases of pneumonia with unknown causes were reported. It quickly reached the state epidemy in numerous countries before being declared a pandemic by the WHO by the 12th of march1. This disease is caused by the SARS-COV-2 virus which name stands for Severe Acute Respiratory Syndrom Coronavirus 2 and give quite a good overview of the symptoms it can produces.

Most people who have the virus only suffers really light, flu-like symptoms, and don’t need hospitalisation nor treatment. However, for some patients, the virus can cause far more trouble, especially in their respiratory system.

In this chapter, we will study the impact of the virus on the respiratory system and learn about how those pathologies are treated in the hospital settings.

What’s going on with the respiratory system?

When the virus gets into the body, it infects healthy cells and use them to produce more virus. See this course to learn more about viruses and the immune system. The virus then progressively migrates from the top of the respiratory system to the bottom. The virus starts by infecting the trachea, the immune system fights back, and this causes an inflammation. This explains the sour throat and coughs, as the smallest dust can irritate the inflamed throat and trachea.

The virus then continues to spread through bronchi to the alveoli.

When the virus gets into the alveoli, it damages the alveoli themselves, the pneumocytes which are the epithelial cells of the alveoli, and the blood capillaries. All those damages produce debris, which accumulates inside the air sacks membrane. Plasma proteins licking from the damages capillaries adds up to those debris and creates even thicker membranes called hyaline membranes. This is called Diffused Alveoli Damages.

We saw in the last course that the membranes are really thin to allow dioxygen and CO2 do diffuse through. With the hyaline membranes, the gases cannot pass from the alveoli to the capillaries and back. This causes a pathology called ARDS (Acute Respiratory Distress Syndrome) were the patient is hypoxic, meaning he can’t get enough oxygen into his blood and short breathed. ARDS is a very serious and potentially fatal disease.

Figure 1 – Normal lung alveoli (left). Acute exudtive phase of DAD with prominent hyaline membranes (right). Attribution-ShareAlike 2.0 Generic (CC BY-SA 2.0) Yale Rosen

On the left image you can see a microscopy picture of a normal pulmonary alveoli. The white parts are the air sacks which are full of air. The purple lines are the membranes which separate the different alveoli and contains the blood capillaries. Note how thin they are and how big the alveoli are compared to the membrane. On the right-hand side, you can see a microscopy image of a pulmonary alveoli of a patient suffering from ARDS. We can observe that the vast majority of the picture is filled by membranes. The air sacks are also way smaller as the hyaline’s membranes forced them to shrink.

What are the treatments of ARDS?

First of all, the only goal of the treatments and technics presented here is to achieve a sufficient level of oxygenation for the patients. Those treatments won’t actually fix the underlaying problems caused by the virus infection.

The amount of oxygen in the patient blood is measured using a pulse oximeter, it often looks like a little clip that is placed on the tip of a finger. It uses a light beam to measure how much oxygen is in the blood. The value is called SpO2 which stands for “peripheral capillary oxygen saturation”. And is given in percent. For the average person, the SpO2 value is around 98 to 99%.

Figure 2 – Pulse oximeter Thinkpaul / CC BY-SA (

Face mask oxygenation

For patients which suffer from respiratory difficulties, their SpO2 needs to be maintained at 94% or higher. In most cases, patients are just given supplemental oxygen therapy using an oxygen face mask. In this case, the patient still breath totally by its own, but the air inhaled is greatly enriched in oxygen (up to 100% oxygen with a reservoir bag mask, compared to 20% oxygen in ambient air).

High Flow Nasal Oxygenation

If a correct oxygenation of the patient cannot be reached using face mask oxygenation, High Flow Nasal Oxygenation may be employed. As for the previous method, the HFNO allows the patient to breath air with high oxygen concentration, but in this case, the air is pressurized which helps for a better oxygen assimilation. However, this method is said to be an aerosol generating procedure, which means that the high flow rate shoots germs and viruses from the patient. This procedure should thus be realized with important PPE from the staff and if possible, in a positive pressure room. The same precaution and security measures will also need to be considered for the following treatments.

Mechanical ventilation

For more severe cases, patients require to be placed in Intensive care Units (ICU) and provided with mechanical ventilation. Mechanical ventilation is different from the previous technics we saw, as the machine will help the patient breathing using positive and negative pressure. When the pressure is positive, the air is pushed into the lungs, which helps or replicate the patient inhalation, and the opposite goes for the ventilation with negative pressure. There are two mains categories of mechanical ventilation which are Invasive (IV) and Non-Invasive (NIV).

Non-Invasive Ventilation

In NIV, the pressurized air is provided using a face mask. It is called noninvasive as no instrument nor tube is placed inside the patient respiratory system. However, it has been proved that NIV can have a high failure rate due to poor mask fit, and often delays the intubation of patients which in most cases will be required anyway due to a degrading condition. NIV should not be a routine technic but as been more and more used in the COVID-19 pandemic as there were not enough Invasive mechanical ventilation material.

Invasive Ventilation

Invasive ventilation is a heavy procedure in which the oxygen is directly outputted into the patient’s trachea. It involves placing an endotracheal tube into the patient trachea from its mouth, or a tracheostomy tube which is directly placed into the trachea by a small incision made in the patient throat. Both technics requires the patient to be highly sedated or placed in artificial comma to provide tolerance of the tube. When the tube has been in inserted into the patient’s trachea, a balloon cuff around the tube is inflated which prevent the tube from moving and allow for a good pressure seal.

Patients placed in ICU due to COVID-19 often require at least 2 weeks of mechanical ventilation, unconscious, in artificial comma, fed by perfusion. Patients will lose a lot of muscle mass and require weeks of rehabilitation.

[patients] tend to come out weak, forgetful, confused, deconditioned, maybe not even able to get out of bed.

 Dr. Kenneth Lyn-Kew for the Scientific American journal

Prone positioning

In addition to mechanical ventilation, patients are usually placed in a prone position (face down). Due to the shape of the lungs, this position relieve pressure caused by the gravity onto the base of the lungs and allow the alveoli to take in more air. Additionally, the prone position allows the heart to rest on the sternum and not on the lungs, which once again relieves pressure on the lungs. To learn more about prone positioning in ARDS patient you can watch this video.


Another procedure which is sometimes employed for extremely ill patients whose lungs are too damaged is the ECMO (Extra corporal membrane oxygenation). The procedure consists in connecting the patient’s arteries and veins (usually femoral) during a surgical operation to a machine which will oxygenate the patient’s blood before pumping it back into its body. This technic was first used in heart and lungs surgery in operating rooms, and more recently used in the prehospital settings (in France) in the case of cardiac arrests with the intention of replacing the heart until further medical cares are provided. ECMO was proved to be really efficient in the treatment of MERS infected patients in 2012 but results for COVID-19 appears to be significantly lower (94.1% vs. 65.0% mortality rate)4. Those results are not fully understood yet and further research needs to be conducted.

That is the end of this course. Please stay at home and follow your local gouvernement’s directives.

1 – WHO announces COVID-19 outbreak a pandemic [Internet]. 2020 [cited 2020 Apr 4]. Available from:

2 – A Pulmonary Pathologist’s Perspective on COVID-19 [Internet]. [cited 2020 Apr 12]. Available from:

3 – Xu Z, Shi L, Wang Y, Zhang J, Huang L, Zhang C, et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. The Lancet Respiratory Medicine. 2020 Feb 1;8.

4 – Henry BM, Lippi G. Poor survival with extracorporeal membrane oxygenation in acute respiratory distress syndrome (ARDS) due to coronavirus disease 2019 (COVID-19): Pooled analysis of early reports. J Crit Care [Internet]. 2020 Apr 1 [cited 2020 Apr 12]; Available from:

5 – Respiratory Management of COVID 19 [Internet]. Physiopedia. [cited 2020 Apr 12]. Available from: