THE 2019 Coronavirus Disease (COVID-19) and its Causative Agent SARS-CoV-2

GUIDE TO INFECTION CONTROL IN THE HEALTHCARE SETTING

THE 2019 CORONAVIRUS DISEASE (COVID-19) AND ITS CAUSATIVE AGENT, SARS-CoV-2

Authors: Jaffar A. Al-Tawfiq, MD, FRCP, FACP, & Ziad A. Memish, MD, FRCPC, FACP
Chapter Editor: Gonzalo Bearman, MD, MPH

Chapter last updated: September 2023
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KEY ISSUES

The Coronavirus Disease (COVID-2019) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). SARS-CoV-2 emerged in Wuhan city, Hubei, China in December 2019. The initial event was related to a cluster of pneumonia cases associated with a seafood market, a wet food market where many different products apart from seafood were sold.  The outbreak was reported officially to the World Health Organization (WHO) at the end of December 2019 following the isolation of SARS-CoV-2 from the affected patients. The virus causing COVID-19 was named SARS-CoV-2 and was classified as belonging to lineage B of the genus Betacoronavirus and was closely related to the known SARS-CoV. Soon, the genomic sequence of this virus was made available to scientists worldwide. The virus caused a global pandemic as declared by the WHO on March 11, 2020. The pandemic had caused significant disruption globally and was declared over as per WHO on May 5, 2023, following the 15th meeting of the Emergency Committee. The diseases at that time had caused 765,222,932 global infections including 6,921,614 deaths.

KNOWN FACTS

  • COVID-19 emerged in Wuhan city, Hubei Province, China in December 2019.
  • The etiology of COVID-19 is SARS-CoV-2, a Betacoronavirus closely related to the known SARS-CoV.
  • The intermediate host had not been identified yet.
  • The incubation period for COVID-19 is within 14 days, generally 4-5 days, and is about 3 days for the Omicron (B.1.1.159) variant.
  • Mild disease: 81%
  • Severe cases: 14%
  • Critical disease: 5%
  • Recognition of the COVID-19 epidemic was important, and the credit goes to Chinese scientists including the late ophthalmologist Dr Li Wenliang, one of the eight physicians who alerted the world of an outbreak of pneumonia of unknown cause. In addition, the web-based international surveillance system for emerging pathogens—ProMED-mail—had reports of cases of undiagnosed pneumonia resembling SARS weeks before the World Health Organization (WHO) reported the epidemic.
  • Data on the rate of infection among healthcare workers had received special attention and research showed that HCWs accounted for 3.8% to 19% of all cases.

CONTROVERSIAL ISSUES

  • The contribution of the transmission route to the spread of the SARS-CoV-2 is controversial. However, it is agreed that the virus spreads through respiratory droplets and contact routes.
  • It is possible that droplet nuclei transmission (airborne) may occur during aerosol-generating procedures especially where ventilation is poor.
  • It is possible that environmental contamination plays a role in transmission, particularly via hands being contaminated by droplets on surfaces.
  • Routine cleaning and disinfection are suitable for maintaining a safe environment in healthcare settings.

SUGGESTED PRACTICE

It is important to realize and adhere to the routine practice of early identification, triaging suspected patients, and prompt isolation similar to other respiratory viral infections. In healthcare facilities, in the absence of aerosol-generating procedures, face masks, gloves, and aprons are recommended. Respirators are recommended in situations where an aerosol-generating procedure (AGP) (such as suctioning, intubation, or nebulization therapy) is undertaken taking a nasopharyngeal swab is an AGP and a respirator is recommended due to the close proximity and cough or gag reflex being stimulated. The World Health Organization (WHO) states that health workers who collect nasopharyngeal and oropharyngeal swabs use appropriate PPE (i.e., eye protection, a medical mask, a long-sleeved gown, and gloves). If the specimen is collected with an AGP (e.g., sputum induction), the personnel conducting the procedure should wear a particulate respirator at least as protective as a NIOSH-certified N95, an EU standard FFP2, or an equivalent respirator.

It is important to keep in mind that the use of gloves does not substitute hand hygiene. Gowns and eye protection should be used as well as hair covers if available. It is preferable to place the patient in a room with negative air pressure, especially during AGP. In low-middle income countries, negative pressure rooms might not be available and thus it is prudent to increase rooms’ natural ventilation to the following minimum hourly average ventilation rates of 160 l/s/patient (hourly average ventilation rate) for airborne precaution rooms (with a minimum of 80 l/s/patient).

Table 1: Management of Suspected of having COVID-19 

  • Isolate the patient.
  • Place the patient in a private room with negative pressure, if possible.
  • In low-middle income countries, negative pressure rooms might not be available and thus it is prudent to increase rooms’ natural ventilation to the following minimum hourly average ventilation rates of 160 l/s/patient (hourly average ventilation rate) for airborne precaution rooms (with a minimum of 80 l/s/patient).
  • Wear gloves, a gown, and a medical mask and if an aerosol-generating procedure (AGPs) is to be undertaken, use an N-95 respirator. Some AGPs have been associated with increased risks of transmission of SARS-CoV-2. According to the WHO, these AGPs include tracheal intubation, non-invasive ventilation (e.g., BiPAP, CPAP), tracheotomy, cardiopulmonary resuscitation, manual ventilation before intubation, bronchoscopy, sputum induction induced by using nebulized hypertonic saline, and autopsy procedures. It remains unclear whether aerosols generated by nebulizer therapy or high-flow oxygen delivery are infectious.
  • Perform these AGPs in an adequately ventilated room or a negative pressure room.
  • Remove the gown, mask, and gloves and discard them in the room before leaving.
  • Carry out hand hygiene- ABHR or hand washing.
  • Open the door and come out of the room.
  • Carry out hand hygiene.
  • Carefully remove the respirator outside the patient’s room without contaminating hands.
  • Perform hand hygiene after removing gloves, and as indicated, and apply the WHO’s “My 5 Moments for Hand Hygiene”.
  • Limit the number of healthcare workers caring for patients and track them.
  • Limit the number of visitors to those who need visitors such as children and critically ill patients.
  • Perform bacterial and viral diagnostic studies for community-acquired pneumonia including SARS-CoV-2
  • Maintain a clean and dry environment with daily cleaning with soap and water and wiped over with 70% alcohol wipes for all surfaces in the healthcare zone.
  • Use 70% alcohol on bedside counters and on medical equipment that can tolerate the disinfectant, such as IV poles, at least daily. Note that chlorine is corrosive and an irritant for the respiratory tract thus making clinical symptoms worse.
  • Supplement oxygen for hypoxemia.
  • Use antibacterial agents if secondary community-acquired pneumonia has been diagnosed.
  • Use a neuraminidase inhibitor for the treatment of influenza.
  • Symptomatic patients with non-severe disease and at increased risk of complications such as older (> 65 years, presence of comorbidities, or immunocompromised): use Nirmatrelvir-ritonavir if no contraindication. Be aware of significant drug-drug interactions. For severe disease and those with hypoxia: use steroids such as dexamethasone.
  • For hospitalized patients without hypoxia: the use of remdesivir is a reasonable choice.
  • Stay updated with the COVID-19 vaccine.
  • Have source control and thus those with suspected or confirmed SARS-CoV-2 infection or other respiratory infection (e.g., those with a runny nose, cough, or sneeze) should have a face mask.

SUGGESTED PRACTICE IN UNDER-RESOURCED SETTINGS

Table 2: Management of Suspected COVID-19 Patients

  • Isolate the patient and ensure that at least minimum requirements for infection prevention and control are in place as soon as possible.
  • Applying standard precautions for all patients.
  • Place the patient in an adequately ventilated single room.
  • Wear gloves, a gown, and regular surgical masks (N-95, especially when performing aerosol-generating procedures).
  • Just before leaving the room, remove the gown, mask, and gloves in the room. Discard in an infectious waste container.
  • Perform hand hygiene after removing gloves, and as indicated, and should apply the WHO’s “My 5 Moments for Hand Hygiene”.
  • Limit the number of healthcare workers caring for patients.
  • Limit the number of visitors.
  • Perform diagnostic studies, if possible, to rule out known causes of community-acquired pneumonia and to rule out COVID-19 disease, SARS-CoV-2.
  • Maintain a clean environment. Use 70% alcohol on bedside counters and on medical equipment that can tolerate the disinfectant, such as IV poles, at least daily. Note that chlorine is corrosive and an irritant for the respiratory tract thus making clinical symptoms worse.
  • Supplement oxygen for hypoxemia.
  • Antibacterial agents for community-acquired pneumonia.
  • Consider a neuraminidase inhibitor for the treatment of influenza, if available.
  • For severe disease and those with hypoxia: use steroids such as dexamethasone.
  • Stay updated with the COVID-19 vaccine.
  • Have source control and thus those with suspected or confirmed SARS-CoV-2 infection or other respiratory infection (e.g., those with a runny nose, cough, or sneeze) should have a face mask.

Environmental cleaning and disinfection: It is important to ensure proper and frequent cleaning and disinfection of surfaces and the environment.   However, cleaning environmental surfaces with water and detergent and using common hospital disinfectants (e.g., sodium hypochlorite) are effective and sufficient.

Table 3: Discontinuation of Droplet and Airborne Isolation Precautions in All Settings

  • Symptomatic patients: resolution of symptoms with no fever and no respiratory symptoms.
  • Patients with severe illness and those who are immunocompromised: consider extending the period to 20 days.
  • Currently, serologic testing is not indicated to establish the presence or absence of SARS-CoV-2 infection or reinfection.

SUMMARY

The COVID-19 disease has caused a global pandemic since 2020, ending in May 2023. The disease is caused by SARS-CoV-2. This virus is phylogenetically distinct from previously known human and animal coronaviruses but is closer to the SARS virus. The SARS-CoV-2 virus was first identified in Wuhan city, Hubei, China in December 2019. It emerged in Southern China in November 2002 and caused a large global outbreak. It spreads from person to person by droplets and contact direct or indirect, as well as possible airborne infection.

REFERENCES

  1. https://promedmail.org/promed-post/?id=20191230.6864153
  2. Centers for Disease Control and Prevention. Interim Infection Prevention and Control Recommendations for Healthcare Personnel During the Coronavirus Disease 2019 (COVID-19) Pandemic. https://www.cdc.gov/coronavirus/2019-ncov/hcp/infection-control-recommendations.html
  3. World Health Organization. Infection prevention and control during health care when coronavirus disease (‎COVID-19)‎ is suspected or confirmed. https://www.who.int/publications/i/item/WHO-2019-nCoV-IPC-2021.1
  4. European Centers for Disease Control and Prevention. Infection prevention and control and preparedness for COVID-19 in healthcare settings https://www.ecdc.europa.eu/sites/default/files/documents/Infection-prevention-and-control-in-healthcare-settings-COVID-19_6th_update_9_Feb_2021.pdf
  5. Tran K, Cimon K, Severn M, Pessoa-Silva CL, Conly J. Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review. PLoS One. 2012;7(4):e35797-e