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Emerging Respiratory Pathogens

Middle east respiratory syndrome coronavirus infection: MERS COV Coronavirus disease-19 (COVID-19) MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS INFECTION: MERS COV ICD-10 code: B34.2/J16.8 + (B97.2) *Notifiable medical condition. Note: Consult most recent guidelines from the National Department of Health/ NICD. DESCRIPTION  Middle East Respiratory Syndrome (MERS) is a viral respiratory illne

Middle east respiratory syndrome coronavirus infection: MERS COV

Coronavirus disease-19 (COVID-19)


MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS INFECTION: MERS COV

ICD-10 code: B34.2/J16.8 + (B97.2)

*Notifiable medical condition.


Note:

Consult most recent guidelines from the National Department of Health/ NICD.


DESCRIPTION 

Middle East Respiratory Syndrome (MERS) is a viral respiratory illness caused by Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Individuals with MERS-CoV present with a wide spectrum of clinical presentation, ranging from asymptomatic infection to acute upper respiratory illness and rapidly progressing lower respiratory illness, respiratory failure, septic shock, and multi-organ failure resulting in death.

A typical presentation of MERS includes:

  • Fever (>38°C)
  • Chills or rigors
  • Cough
  • Shortness of breath

Presentation may also include haemoptysis, sore throat, myalgias, diarrhoea, vomiting, and abdominal pain.

Complications:

  • Severe pneumonia
  • Acute renal failure
  • ARDS
  • Refractory hypoxaemia

GENERAL MEASURES

  • Ensure that patients suspected to have MERS Coronavirus are isolated at all times to limit further exposure.
  • Discuss and manage all suspected, probable cases and contacts in consultation with the regional virologist or infectious diseases specialist at the referral centre/NICD.
  • Transfer of patients should only occur once all relevant arrangements have been made to limit further exposure to a potential contagious and life threatening agent.
  • Record and follow-up all patient contacts.

Prevention

  • Practise handwashing and careful disposal of materials that are infected with nasal secretions.
  • Use antiseptic/disinfectant solutions containing choroxylenol, benzalkonium chloride, and/or cetrimide. Chlorhexidine has been shown to be ineffective.
  • Add droplet precautions to the standard precautions. Airborne precautions should be applied when performing aerosol-generating procedures.

MEDICINE TREATMENT

  • Treatment is supportive.
  • No antiviral agents or vaccines are currently available.

REFERRAL

  • All cases after consultation with infectious diseases specialist and NICD.

CORONAVIRUS DISEASE-19 (COVID-19)

ICD-10 code: U07.1/U07.2

*Notifiable medical condition.


Note:
Consult the most recent NICD guidelines on the clinical management of suspected or confirmed Covid-19 disease, available at: https://www.nicd.ac.za/diseases-a-z-index/disease-index-covid-19/covid-19- guidelines/clinical-management-of-suspected-or-confirmed-covid-19-disease/


DESCRIPTION

Coronavirus Disease of 2019 (COVID-19) is a viral, respiratory illness caused by SARS-CoV-2. Infection may be asymptomatic, and the majority of symptomatic infections (>80%) are characteristed by mild upper- and/or lower respiratory tract symptoms. However, a minority of patients may develop severe disease requiring supplementary oxygen or, in severe cases, mechanical ventilation.

A typical presentation of COVID-19 includes some or all of the following:

Complications:

  • Refractory hypoxaemia
  • ARDS
  • Long-COVID
  • MIS-C and MIS-A

Diagnosis

Samples should be sent for SARS-CoV-2 PCR testing. Upper respiratory tract samples from all suspected patients should be sent – a nasopharyngeal swab is preferred, but in patients where this is not possible (e.g. recent nasal surgery, or severe coagulopathy), an oropharyngeal, nasal mid-turbinate, or anterior nares swab can be collected instead. Lower respiratory tract samples (e.g. sputum, tracheal aspirates) may be sent in addition if available.

GENERAL MEASURES

  • If COVID-19 is suspected, isolate patient to limit further exposure.
  • Adhere to standard contact and droplet precautions.
  • Apply precautions against airborne transmission when performing aerosol-generating procedures such as intubation or nasogastric suctioning.

Management

  • Give supplemental oxygen if required, targeting an SpO2 of ≥90% for non-pregnant adults (≥94% for pregnant women). Titrate oxygen therapy to reach targets by means of a nasal cannula, simple face mask or face mask with a reservoir bag, as appropriate.
  Nasal cannula Simple face mask Face mask with reservoir bag
Flow rate 1-5 L/min 6-10 L/min 10-15 L/min
FiO2 estimate 0.25-0.4 0.4-0.6 0.6-0.95
  • Patients who have respiratory failure despite maximal face mask oxygen should be promptly identified and considered for possible escalation of respiratory support with high flow nasal cannula oxygen, continuous positive airway presure, or intubation and mechanical ventilation as appropriate.
  • The use of the prone position in non-intubated, conscious patients who are hypoxaemic may be beneficial.

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MEDICINE TREATMENT


Note:

Antibiotics are of no value for the treatment of confirmed COVID-19 unless there is clear evidence of a co-existing infection.


Thromboprophylaxis:
ICD-10 code: 
(Z29.2)

All hospitalised patients with COVID-19 require prophylaxis against venous thromboembolic disease, in the absence of any contraindications (see: Venous thrombo-embolism).

  • Low molecular weight heparin, e.g.:

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  • Enoxaparin, SC, 40 mg daily.
    • Reduce dose to 20 mg daily in patients with renal failure (eGFR <30 mL/minute).

OR

  • Unfractionated heparin, SC, 5 000 units 12 hourly.

Note:

Patients with D-dimer >1.5 mg/L or requiring a non-rebreather mask or more should be considered for therapeutic doses of LMWH or unfractionated heparin (see: Venous thrombo-embolism).


  • Low molecular weight heparin, e.g.:

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  • Enoxaparin, SC, 1.5 mg/kg daily,

OR

  • Enoxaparin, SC, 1 mg/kg 12 hourly.

In morbid obesity, dosing of LMWH should be individualised in discussion with a specialist.

In renal failure (eGFR <30 mL/minute), the recommended therapeutic dose of LMWH is 1 mg/kg daily.


Evidence indicates that PTT monitoring is not necessary with weight-based dosing of unfractionated heparin.
However, in patients with morbid obesity and renal failure (eGFR <30 mL/minute), unfractionated heparin should be used with PTT monitoring to maintain the PTT at 1.5 to 2.5 times the control. PTT should be taken 4 hours after SC dose.


In non-pregnant patients who require supplemental oxygen:

  • Corticosteroids, e.g.:
    • Dexamethasone, IV, 6 mg daily for up to 10 days, or until discharge.

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In pregnant patients who require supplemental oxygen:

If corticosteroids are also needed to accelerate foetal lung maturity: See: Preterm labour (PTL) and preterm prelabour rupture of membranes (PPROM).

If corticosteroids are not needed for foetal lung maturity:

  • Corticosteroids, e.g.:
    • Dexamethasone, IV, 6 mg daily for up to 10 days, or until discharge.

If there is a concern of in-utero steroid exposure, use corticosteroid therapy with less placental transfer:

  • Prednisone, oral 40 mg daily, for up to 10 days, or until discharge.

OR

  • Hydrocortisone, IV, 80 mg 12 hourly for up to 10 days, or until discharge.

Note:

- See: COVID-19 in pregnancy.

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Corticosteroids cross the placenta and may have long-term, deleterious effects on the child. 


Click here to access the pdf.


Standard Treatment Guidelines and Essential Medicines List for South Africa, Adult Hospital Level, 2020-2024_Version 1.2_20 January 2025

Chapter 9 Systemic and Healthcare-Associated Infections_9.4 Emerging Respiratory Pathogens

Drugs mentioned

ICD-10 codes

NeoHealth® ID 17946 · updated 7/4/2025