(Coronavirus disease 2019)

Abstract: COVID-19, also known as coronavirus disease 2019, is a respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Transmission mainly occurs via direct contact or respiratory droplets. The infection may present asymptomatically, as a mild “flu-like” illness, or severely, with shortness of breath and life-threatening complications. Individuals who are over 65 years of age, immunosuppressed, or have preexisting conditions have a higher risk of developing severe symptoms and complications. Management is based on supportive care.

Updated December 1, 2020

Coronaviruses viewed under an electron microscope. Note the characteristic crown-like (corona) appearance
Image: by CDC/ Dr. Fred Murphy, License: Public Domain Files

Table of Contents

Share this concept:

Share on facebook
Share on twitter
Share on linkedin
Share on reddit
Share on email
Share on whatsapp

Table of Contents


Coronaviruses (CoVs) are a family of enveloped, positive-sense, single-stranded RNA viruses. They tend to cause mild upper respiratory diseases in humans. Of the 7 known species of CoV, only 3 are known to cause severe infections in humans, all within the betacoronavirus genus:

  • Severe acute respiratory disease coronavirus (SARS-CoV): emerged in 2003 in southern China from civet cats
  • Middle East respiratory syndrome coronavirus (MERS-CoV): emerged in 2012 in Saudi Arabia from dromedary camels
  • SARS-CoV-2: emerged in November 2019 in China from bats (still under investigation)
    • The genome is 96.2% identical to bat coronavirus RaTG13.
    • A widely accepted theory is that the pandemic originated in the Huanan seafood “wet” market in Wuhan, China, which is known for the sale of wild animals and their meat, through an unknown intermediate host.
    • Another theory, the Mojiang Miners Passage (MMP) hypothesis, claims that SARS-CoV-2 evolved from RaTG13, a pathogenic coronavirus that infected 6 mineshaft workers in April 2012. 
      • It is proposed that in situ viral passaging enabled the rapid evolution of the virus without the need for an intermediate host. This would constitute a natural human experiment in viral passaging, which is a virological technique for adapting viruses to new species or tissues. The theory is supported by the long infectious period experienced by 3 of the miners (at least 57–120 days).
      • These patients presented with a mysterious, severe respiratory illness closely resembling COVID-19; 3 of the miners eventually passed away.
      • The virus from the infected miners had reportedly been sent to the high-level laboratory of Zheng-li Shi at the Wuhan Institute of Virology (WIV). This facility received the highest laboratory biosafety accreditation (BSL-4) in 2018, which coincides with the beginning of its active research on the virus.
      • The virus is believed to have escaped the WIV where it was being studied. The escape of a pathogen from a high-level infectious disease laboratory has occurred numerous times and in many countries. There are 5 basic routes of escape: aerosolization, accidental exposure, fomites, accidental animal or vector release, or deliberate release.

Selected diseases caused by Coronaviruses

 Common coldGI tract infectionSevere acute respiratory syndrome (SARS)COVID-19 (Wuhan, China)
Incubation3 days3 days4–6 days2–14 days
IncidenceMost commonRareRareCurrent pandemic
PrognosisComplete resolutionComplete resolution
(up to 25% fatal for NEC)
30% resolution
70% severe infection
10% fatal
80% resolution
15% severe case
5% critical case
2.3% fatal (based on confirmed cases as of Dec 1, 2020, may change)
Clinical manifestationSneezing, rhinorrhea, headache, sore throat, malaise, fever, chillsDiarrhea, gastroenteritis, neonatal necrotizing enterocolitis

Fever > 37,8°C (100,0°F), muscle pain, lethargy, cough, sore throat, malaise

Shortness of breath/ pneumonia (direct viral or secondary bacterial)


Mild infection: fever, dry cough, malaise, dehydration

Severe infection: high fever, shortness of breath, chest pain, hemoptysis

Complications: pneumonia, ARDS, sepsis, multi-organ failure

Diseases caused by Coronaviruses

 Common ColdGI tract infection
Incubation3 days3 days
IncidenceMost commonRare
PrognosisComplete resolutionComplete resolution(up to 25% fatal for NEC)
Clinical manifestationSneezing, rhinorrhea, headache, sore throat, malaise, fever, chillsDiarrhea, gastroenteritis, neonatal necrotizing enterocolitis
 Severe acute respiratory syndrome (SARS)2019 nCoV (Wuhan City, China)
Incubation4–6 days2–14 days
IncidenceRareCurrent pandemic
Prognosis30% resolution
70% severe infection
10% fatal

80% resolution
15% severe case
5% critical case
2.3% fatal (as of Dec 1, 2020, based on identified cases and may change)

Clinical manifestation

Fever > 37,8°C (100,0°F), muscle pain, lethargy, cough, sore throat, malaise

Shortness of breath/ pneumonia (direct viral or sencondary bacterial)

Mild infection: fever, dry cough, muscle pain, lethargy, dehydration

Severe infection: high fever, shortness of breath, chest pain, hemoptysis

Complications: pneumonia, ARDS, sepsis, multi-organ failure

NEC: Necrotizing enterocolitis ARDS: Acute respiratory distress syndrome

The SARS-CoV-2 virion is approximately 125 nm in diameter and its genome ranges from 26–32 kb, the largest of all RNA viruses. It has 4 structural proteins: spike (S), envelope (E), membrane (M), and nucleocapsid (N).

  • S, E, and M proteins create the viral envelope. 
  • N protein forms a complex with RNA (nucleocapsid) and aids in the regulation of viral RNA synthesis.
  • M protein projects on the external surface of the envelope, spans the envelope 3 times, and is important for viral assembly. 
  • E protein has an unclear function, although it may aid in viral release.
  • S protein is a club-shaped surface projection, giving the virus its characteristic crown-like appearance on electron microscopy. It is responsible for receptor binding and fusion with the host cell membrane.
Structural proteins of the SARS-CoV 2 virion.
Image: by Lecturio

In January 2020, population genetic analysis concluded that SARS-CoV-2 had evolved into 2 separate genotypes: 

  • L type: more aggressive and more prevalent (approximately 70% of cases in the early stages of outbreak; prevalence has since decreased) 
  • S type: evolutionary older, less common, and less aggressive (approximately 30% of cases)

Lecturio resources


Coronaviruses are zoonotic; that is, they are transmitted to humans through animals. It is hypothesized that horseshoe bats are the natural reservoir of SARS-CoV-2 since the virus’s genome is 96.2% identical to that of a bat coronavirus. At this time, the intermediate host is still unknown, and the MMP theory of origin does not require the existence of one.

Once in humans, the virus is transmitted when respiratory droplets or aerosolized particles from infected individuals come into direct contact with the mucous membranes of another individual, including the eyes, nose, or mouth. In the air, larger droplets tend to drop toward the ground, within 1 m (3 ft) of the infected person, while smaller droplets can travel over 2 m (6 ft) and remain viable in the air for up to 3 hours under certain conditions. Other forms of transmission include the following:

  • Direct transmission through hand-to-face contact from infected surfaces
  • Transmission in bodily fluids. Although SARS-CoV-2 has been detected in stool specimens, blood, ocular secretions, and semen, the possibility of transmission through these routes remains uncertain.
  • Vertical transmission (mother to child):
    • Has been reported in several cases of peripartum maternal infection in the 3rd trimester. However, most neonatal infections are thought to result from postnatal exposure through respiratory droplets from an infected mother or caregivers. Neonates present asymptomatically or with mild disease.
    • A case of transplacental transmission of SARS-CoV-2 has been reported due to maternal infection in the third trimester. The neonate required neonatal resuscitation and presented with neurological compromise. Congenital infection was proven via viral detection in the amniotic fluid collected prior to the rupture of membranes and in blood samples within the first 6 hours of life.
Covid-19 Coronavirus disease 2019

Whether COVID-19 has airborne or droplet/contact transmission is a topic still under study and of debate.

Droplet or contact transmission is defined as the transmission of infectious viral particles from an infected person to a new host through large respiratory droplets (> 5μm in diameter), either via the touching of a contaminated surface or contact with these droplets in the air. Airborne transmission differs in that it includes small respiratory droplets (< 5μm in diameter; also called droplet nuclei) that can remain suspended in the air for long periods of time, negating the need for close contact between individuals.

The main difference between these modes of transmission is the size of the droplets, which, in turn, dictates how long they can remain in the air, how far they can travel, and how many virions they can carry (making the droplets more or less infectious). As a general rule, larger droplets fall to the ground within 1–2 meters (3–6 feet) of its source, while aerosol droplets can overcome the force of gravity. It is also commonly believed that coughing and sneezing generate large-droplet emission, while only aerosol-generating procedures can emit small droplets.

However, upon further research on the spread of COVID-19, it is now clear that the distinctions between airborne and droplet/contact transmission are not as rigid as earlier believed. Once emitted into the air, large droplets can evaporate to form small aerosol droplets. Studies have shown that even talking and normal breathing can generate droplets and aerosols. In one recent study, it was shown that virus particles can reach 0.84 meters in 5.5 seconds. How far these droplets (both large and small) can travel, however, is also affected by environmental factors such as humidity, temperature, ventilation pattern and rate, the velocity of emission, and droplet composition.

There is continuing debate about the proportion of new infections caused by respiratory droplet/contact transmission versus the airborne route. Aerosols are suggested as the dominant mechanism of transmission since most outbreaks occur in closed environments, while outbreaks are rare in outdoor environments as they do not favor the dispersion of small aerosol particles. It is also possible that some asymptomatic individuals, or so-called “superspreaders,” have an increased capacity to generate aerosols via normal talking and breathing.

Covid-19 Coronavirus disease 2019

Many factors can extend the range of respiratory droplet dispersion past 2 meters. Certain actions, such as forced expiration during yelling, singing, and exercise, can increase the volume of droplets emitted and the distance these droplets can travel.

It should also be noted that small aerosol doses are less likely to cause illness, even if the exact infectious dose for COVID-19 is still unknown. The detection of viral RNA in the air does not guarantee the possibility of human infection. However, certain medical procedures can generate virus-laden aerosol clouds that put healthcare personnel at higher risk of becoming infected. (See “Prevention” for more information on aerosol-generating procedures.)

The reproductive number (R0), or the number of secondary infections generated from 1 infected individual, is 2–2.5, higher than for influenza (0.9–2.1). However, the R0 can vary widely (it was calculated as 5.7 in the early phases of the pandemic in China, and in some nursing homes in the United States) because it depends on both host and viral factors. 

COVID-19 is highly contagious for the following reasons: 

  • Production of high viral loads
  • Efficient and prolonged shedding of virions from the upper respiratory tract
  • Asymptomatic individuals are also infectious, posing a significant challenge for contagion prevention. 
    • Viral loads peak before symptom onset, leading to asymptomatic or presymptomatic spreading of the virus and making symptom-based detection and isolation ineffective. 
    • Asymptomatic patients can produce high viral loads in secretions of the upper respiratory tract and can shed the virus for the same amount of time as symptomatic patients.
  • SARS-CoV-2 can remain infectious on surfaces outside of a host from a few hours to a few days.
    • The viral lifespan depends on the type of surface, temperature, and humidity levels.
    • There is currently no evidence to suggest that COVID-19 can be acquired from mail and packaged goods but caution is still advised.
Image: by Lecturio, Source: The Journal of Hospital Infection
Covid-19 Coronavirus disease 2019

The period of infectivity for symptomatic cases is currently believed to range from 3 days before the onset of symptoms up to 3 days after their resolution if symptom onset was > 10 days prior. The exact limits of infectivity are still under investigation.

The median duration of viral RNA shedding from the upper respiratory tract is 20 days. Viral shedding can outlast the resolution of symptoms. Some studies have reported viral detection in stool samples up to 35 days after the onset of symptoms (approximately 25 days after symptom resolution). However, the detection of viral RNA does not necessarily indicate the presence of an infectious virus. It has been shown that the more severe the case, the longer the patient will continue to shed the virus after recovery. 

Studies have also shown that recovered COVID-19 patients generate a significant CD4+ and  CD8+ T cell response against SARS-CoV-2. Seroconversion, or the production of COVID-19-specific antibodies, occurs after 7 days in 50% of patients and by day 14 in all patients. However, it is still unclear to what degree antibodies provide a protective effect or if reinfection is possible.


The first case of COVID-19 was traced back to the city of Wuhan, China, in late November 2019, with an outbreak developing in December. The virus quickly spread, with widespread ongoing transmission occurring globally. The COVID-19 outbreak was declared a Public Health Emergency of International Concern on January 30, 2020, and a pandemic on March 11, 2020, by the World Health Organization (WHO). Currently, COVID-19 has been reported in every continent except Antarctica, with more than 62 million people infected worldwide and over 1.4 million reported dead within the first year of global spread.

Coronavirus COVID-19 Global Cases by Johns Hopkins CSSE.


SARS-CoV-2 attaches to the host cell by binding its S protein to the receptor protein, angiotensin-converting enzyme 2 (ACE2). ACE2 is expressed by epithelial cells of the intestine, kidney, blood vessels, and, most abundantly, in type II alveolar cells of the lungs. The human enzyme transmembrane protease, serine 2 (TMPRSS2), is also used by the virus for S protein priming and to aid in membrane fusion. The virus then enters the host cell via endocytosis.

SARS-CoV-2 affects the expression and presentation of ACE2, contributing to its pathogenesis in the following ways:

  • Viral entry causes internalization of the receptor, leading to its reduced availability on the cell surface. 
  • ACE2 inhibition induces ADAM17 gene expression, leading to the release of tumor necrosis factor α (TNFα) and cytokines such as interleukin 4 (IL-4) and interferon γ (IFNγ).
  • Increased cytokine concentrations activate further proinflammatory pathways, leading to a cytokine storm.
  • ADAM-17 also promotes the cleavage of ACE2 receptors.
  • SARS-CoV-2’s affinity for ACE2 also results in direct and acute injury to the lung, heart, endothelial cells, and, potentially, other organs.
    • ACE2 is a negative regulator of the RAAS system, its downregulation directly affects cardiovascular function.
    • ACE2 has a direct protective role in alveolar epithelial cells; its reduction leads to alveolar cell damage
Covid-19 Coronavirus disease 2019

High levels of ACE2 expression are associated with certain chronic conditions, especially cardiovascular disease, and are linked to a higher risk of severe cases of COVID-19.

The expression of ACE2 is significantly increased through the use of ACE inhibitors or angiotensin II receptor blockers (ARBs). Contrary to initial reports, it has now been proven that the use of ACE inhibitors and ARBs is not associated with the risk of hospitalization or mortality among those infected with SARS-CoV-2. However, there is an approximately 40% lower risk of hospitalization associated with their use in the Medicare population in the United States, leading to the theory that the use of ACE inhibitors may help reduce the risk of hospitalization among elderly patients.

Although COVID-19 is a respiratory disease, clinical and pathology reports suggest that severe cases reflect a confluence of vascular dysfunction, thrombosis, and dysregulated inflammation. The development of complications and organ damage may be due not only to direct organ damage caused by the viral infection and local inflammation but also by indirect pathogenic mechanisms, including: 

  • Widespread endothelial damage (endothelialitis) with microangiopathy involving the vascular beds of the lungs, heart, kidneys, liver, and intestines
    • An autopsy study found that the lungs of a patient with COVID-19 had 9 times as many clots as those who died of the H1N1 flu.
  • Thrombosis and disseminated intravascular coagulation (DIC)
  • An atypical inflammatory response
  • Autoimmune phenomena, such as Guillain-Barré syndrome and pediatric inflammatory multisystem syndrome, which is an inflammatory state with clinical features similar to those of Kawasaki disease and toxic shock syndrome


COVID-19 differs from the pathogenesis of influenza in that it produces pulmonary angiogenesis. The lungs of COVID-19 patients have shown distorted vascularity with structurally deformed capillaries. This ability has also been associated with the human cytomegalovirus (HMCV). This virus produces increased endothelial cell proliferation and capillary tube formation and is associated with various vascular diseases (e.g., atherosclerosis, transplant vascular sclerosis, and coronary restenosis). This similarity suggests that there may be a link between the pathogenic mechanisms of SARS-CoV-2 and HCMV.

COVID-19 also triggers cell-mediated immune responses. Studies have identified SARS-CoV-2–specific CD8 and CD4 T cells in 70% and 100% of COVID-19 convalescent patients, respectively. CD4 cells seem to target the M, spike, and N proteins, while CD8 cells mainly target spike and M proteins.

Covid-19 Coronavirus disease 2019

T-cell proliferation has been linked to the immune system’s production of viral-specific neutralizing antibodies, which not only provides a protective effect but also aids vaccine design and evaluation. 

However, SARS-CoV-2–reactive T cells have also been detected in individuals who have no known exposure to the virus and who tested negative to RT-PCR and antigens. Thus, cross-reactive T-cell recognition must exist between SARS-CoV-2 and other types of seasonal coronaviruses that cause the “common cold.” This suggests that common cold coronaviruses may provide a small residual immunity and explains the variability of disease progression and severity (this is still under investigation).

Clinical Presentation

The incubation period for COVID-19 ranges from 2–14 days, with an average of 5 days. 

  • 80% of infections are mild or asymptomatic
  • 15% of infections are severe (requiring oxygen therapy)
  • 5% of infections are critical (requiring intensive care unit [ICU] admission and ventilation)

The proportion of severe and critical-to-mild cases is higher than in influenza infections.

Covid-19 Coronavirus disease 2019

The rate of severe, critical, and fatal cases varies depending on location and age group. Children are symptomatic in < 5% of cases and critical in < 1%, while up to 60% of elderly patients develop critical infections.

It has been recently shown that children < 5 years old with mild-to-moderate COVID-19 symptoms have high amounts of SARS-CoV-2 viral RNA in their nasopharynx compared with older children and adults. Even if this study was limited to the detection of viral nucleic acid, rather than an infectious virus, it is clear that there is a correlation between higher nucleic acid levels and the ability to culture infectious virus.

Asymptomatic cases

  • These individuals can transmit the virus.
  • They represent > 50% of all infections (still under investigation).
  • They do not develop any noticeable symptoms.
  • Anosmia, hyposmia, and dysgeusia have been reported in many laboratory-confirmed cases of patients who were otherwise asymptomatic.
  • It has not been clearly determined how long asymptomatic individuals remain contagious after the initial infection.
  • These individuals can present radiological and laboratory findings characteristically found in symptomatic COVID-19 patients (see “Diagnostics”)

Mild cases

  • May present with dry cough and moderate fever
  • Include common flu-like symptoms such as fatigue, malaise, myalgia, runny nose, nasal congestion, and sore throat
  • Less frequently experience diarrhea, nausea, vomiting, diffuse abdominal pain, productive cough, headache, and muscle or joint pain
  • Have a recovery time of approximately 2 weeks

Dermatologic symptoms have now been associated with 5%–20% of COVID-19 patients
in recent reports. The symptoms include maculopapular rashes involving mainly the truck and associated with viremia, urticarial and vesicular lesions, petechiae/purpura, chilblains, livedo reticularis, and distal ischemia or necrosis. Notably, chilblain-type lesions of the fingers and toes that last 3–4 weeks have also been seen, and have come to be called “COVID toes.”

Covid-19 Coronavirus disease 2019

There are no specific clinical features that can reliably distinguish COVID-19 from other viral respiratory infections such as influenza, SARS, pneumonia, or tuberculosis.

Clinical presentation of COVID-19.
Image: by Lecturio

Severe cases and complications

  • Approximately 1 in 6 people with COVID-19 experience clinical deterioration and/or develop complications in the 2nd week of illness. This is usually marked by the appearance and worsening of dyspnea.
  • Median time from onset of symptoms to the onset of critical care/ICU transfer is 8–9 days.
  • Patients develop dyspnea, high fever, chest pain, hemoptysis, anorexia, and/or respiratory crackles, which indicates the development of pneumonia (the most frequent complication in severe cases).
  • Respiratory failure from acute respiratory distress syndrome (ARDS) is the most common finding in critical cases.
  • Recovery time is approximately 3–6 weeks.
Covid-19 Coronavirus disease 2019

The most common complications include viral pneumonia, respiratory failure and ARDS, sepsis and septic shock, cardiomyopathy, acute kidney injury, and pulmonary thromboembolism. Other complications include acute cardiac injury, deep vein thrombosis, arrhythmia, stroke, liver dysfunction, and multi-organ failure.

Risk factors for a severe infection and development of complications from COVID-19 (from highest to lowest risk) include the following:

  • Age > 65 years 
    • The mortality rate for patients < 65 is < 3%. However, this rises to 3%–11% for individuals aged 65–84 and 10%–27% for individuals ≥ 85 years of age.
  • Living in a nursing home or long-term care facility
  • Chronic diseases:
    • Chronic lung disease or moderate to severe asthma
    • Cardiovascular disease
    • Immunosuppression (from long-term steroid use, cancer, AIDS/HIV infection, congenital immunodeficiency, organ transplants, immunosuppressants, etc.)
    • Severe obesity (BMI > 40)
    • Diabetes mellitus, chronic kidney disease undergoing dialysis, cerebrovascular disease, and liver disease
  • Pregnancy
    • The risk of infection is the same as in non-pregnant individuals.
    • A higher risk of severe illness in pregnant individuals is assumed due to the behavior of similar respiratory infections, such as SARS and influenza.
  • Smoking
    • Recent evidence suggests that smoking is associated with an increased severity of disease and death in hospitalized COVID-19 patients.

Refractory cases

Nearly 50% of COVID-19 patients do not achieve clinical and radiological remission within 10 days of hospitalization. Male patients, older patients, individuals with anorexia, and those with no/low fever at the time of admission have a higher risk of presenting with a refractory progression. Survivors of these infections are likely to be at high risk for pulmonary fibrosis; antifibrotic therapies may be beneficial both in the acute phase of the illness and in preventing long-term complications.

COVID-19 phenotypes

Although the respiratory symptoms and features of COVID-19 are very similar to those of ARDS, COVID-19 differs in 1 key aspect: patients often present with severe hypoxemia associated with near-normal respiratory system compliance. The wide range of possible clinical presentations among COVID-19 patients depends on the interaction between 3 basic factors:

  1. The severity of the infection and the host’s immune response, physiological reserve, and comorbidities
  2. The patient’s responsiveness to ventilatory support for hypoxemia
  3. The period of time between symptom onset and evaluation in a hospital

The interaction of these factors has led to the discovery of 2 COVID-19 phenotypes, which are defined as phases or presentations of the disease that are not distinct types but rather points in a fluid spectrum: 

  • Type L: characterized by normal lung compliance, low ventilation-to-perfusion ratio (normal pulmonary artery pressure), low lung weight (only ground-glass opacities can be seen on imaging), and low recruitability (most of the lung is being aerated)
  • Type H: characterized by low lung elastance, high right-to-left shunt, high lung weight, and high recruitability (increased amount of non-aerated lung tissue)

The progression of a patient from a type L COVID-19 presentation to a type H COVID-19 presentation depends on the worsening of systemic inflammation and interstitial lung edema; thus, worsening their hypoxemia.

COVID-19 in children

The clinical presentation and severity of cases of COVID-19 in patients < 18 years old is different from that of adults. Children are at a lower risk of developing severe or critical infections, and complications appear to be milder.

In children:  
  • Approximately 55% of cases are asymptomatic or mild
  • 40% of cases are moderate (pneumonia and/or abnormal chest imaging)
  • 5% of cases are severe (dyspnea and hypoxia, requiring oxygen therapy)
  • < 1% of cases are critical (ARDS, respiratory failure, shock, or multi-organ failure requiring ICU transfer)
Pediatric inflammatory multisystem syndrome is a newly discovered complication occurring in pediatric patients. The case definition by the Royal College of Paediatrics and Child Health includes the following criteria:
  • A child presenting with persistent fever (≥ 4 days), inflammation (neutrophilia, elevated C-reactive protein, and lymphopenia) and evidence of single- or multi-organ dysfunction (shock or cardiac, respiratory, renal, gastrointestinal, or neurological disorder)
    • This may include children fulfilling full or partial criteria for Kawasaki disease.
  • Exclusion of any other microbial cause, including bacterial sepsis, staphylococcal orstreptococcal shock syndromes, and infections associated with myocarditis (enterovirus)
  • SARS-CoV-2 PCR testing may be positive or negative.

Respiratory symptoms are only present in half of these patients. Abdominal symptoms such as pain, vomiting, or diarrhea are also common.

Lecturio resources


Reverse transcription-polymerase chain reaction (RT-PCR) is currently the only test being used to confirm cases of acute COVID-19 infection and should be performed once a person under investigation (PUI) is identified according to the priorities outlined below. A positive test for SARS-CoV-2 generally confirms the diagnosis of COVID-19, regardless of the patient’s clinical status. The specimens used for testing include the following:

  • Nasopharyngeal (NP) or oropharyngeal (OP) swab
    • NP is the first choice. OP swabs are acceptable only if NP swabs are not available.
  • Nasal mid-turbinate swab or swab of anterior nares (nasal swab)
  • Nasopharyngeal wash/aspirate or nasal wash/aspirate specimen
  • Sputum (for patients with productive cough; inducing is not recommended)
  • Bronchoalveolar lavage, tracheal aspirate, pleural fluid, and lung biopsy (for patients with critical infections receiving invasive mechanical ventilation)

RT-PCR testing can be negative initially. If suspicion of COVID-19 remains, the patient should be retested every 2–3 days. In severe cases, swabs from the upper respiratory tract may be negative, while specimens from the lower respiratory tract are positive. RT-PCR tests can also yield false negatives in 20%–30% of cases. (For further information see the Centers for Disease Control and Prevention’s [CDC’s] “Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19).”)

Image: by Lecturio

1. Nasopharyngeal swab: Insert swab into a nostril parallel to the palate, and carefully slide it forward until a soft resistance is felt. Swab should reach a depth equal to distance from nostrils to outer opening of the ear. Rotate for several seconds to absorb secretions, and then slowly remove. 1. Oropharyngeal swab: Insert swab into the oral cavity without touching the gums, teeth, and tongue. A tongue depressor may be used. Swab the posterior pharyngeal wall using a rotatory motion. 2. Place swabs immediately into sterile tubes containing 2-3 ml of viral transport media. If both swabs are collected, they should be combined into a single vial. 3. Carefully leverage the swab against the tube rim to break the shaft at the scoreline. 4. Store specimens at 2-8°C for up to 72 hours after collection. If a delay in testing/shipping is expected, store specimens at -70°C or below. Use only synthetic fiber swabs with plastic shafts. Calcium alginate swabs or swabs with wooden shafts may inactivate the virus and inhibit PCR testing. 

Covid-19 Coronavirus disease 2019

Due to limited availability of testing in certain countries, a diagnosis of COVID-19 can be made presumptively in the presence of a compatible clinical presentation with an exposure risk, particularly when there is no other evident cause of the symptoms. Testing for other causes of respiratory illness, such as influenza, is strongly encouraged in these cases. However, a positive test result for another respiratory agent does not rule out coinfection.

During an ongoing COVID-19 outbreak, patients with suspected infection who do not present with severe symptoms are encouraged to call prior to presenting to a healthcare facility for evaluation and testing. Laboratory testing of a PUI should be prioritized as follows according to the CDC (only in a state of emergency due to shortages or limited testing capacity):

  • High priority:
    • Hospitalized patients with symptoms
    • Healthcare facility workers, workers in congregate living settings, and first responders with symptoms
    • Residents in long-term care facilities or other congregate living settings, including prisons and shelters, with symptoms
  • Priority:
    • Persons with signs and symptoms compatible with COVID-19
    • Persons without symptoms who are prioritized by health departments or clinicians for any reason, including but not limited to:
      • Public health monitoring
      • Sentinel surveillance
      • Screening of other asymptomatic individuals according to state and local plans

RT-PCR assays are based on nucleic acid amplification, and various types of assays being used around the world detect and amplify different regions of the genome of SARS-CoV-2. The viral genes being targeted include the nucleocapsid (N), envelope (E), spike (S), and the RNA-dependent RNA polymerase (RdRp) gene. Both the RdRP and E genes have high analytical sensitivity for detection, whereas the N gene provides poorer analytical sensitivity. The use of at least 2 molecular targets is required in order to avoid cross-reaction with other endemic coronaviruses. RT-PCR has very high sensitivity and specificity.

Rapid antigen testing, on the other hand, detects specific viral antigens and has the additional advantage of being able to be performed at the point of care. It is particularly useful in the early stages of infection, especially in cases of known exposures. The 2 rapid antigen tests approved by the Food and Drug Administration (FDA) have a specificity of 100%; thus, false-positives are unlikely. However, the sensitivity of these 2 tests is 84% and 97%, significantly lower than RT-PCR (100%). In general, positive antigen tests should be confirmed via an RT-PCR test performed at least 2 days later.

Covid-19 Coronavirus disease 2019

All PUI and confirmed cases should be reported according to the regulations stipulated by local health authorities and the national surveillance center.

Patients with COVID-19 present with the following laboratory and radiological findings. These are more pronounced and common in severe and critical cases but can also be present even in asymptomatic infections:

  • White blood cell count: leukopenia, leukocytosis, and lymphopenia (most common)
  • Inflammatory markers: ↑ LDH and ferritin
  • Liver markers: ↑ AST and ALT 
  • Chest X-ray and computed tomography (CT): 
    • Not recommended for initial evaluation; reserved for hospitalized patients or symptomatic patients with specific clinical indications
    • Common findings include ground-glass opacities (GGOs), multiple areas of consolidation, “crazy paving appearance” (GGOs + inter-/intralobular septal thickening), and bronchovascular thickening.
    • Lesions usually have a bilateral, peripheral, and lower lobe distribution.
Covid-19 Coronavirus disease 2019

Radiological findings associated with COVID-19 are not specific to the infection; they overlap with other respiratory illnesses including influenza, H1N1, SARS, and MERS.

In hospitalized COVID-19 patients with severe infections, regular laboratory testing and imaging are necessary for the assessment of disease progression and complications:

  • Complete blood count: Severe cases present with advanced lymphocytopenia and thrombocytopenia. 
  • Arterial blood gases: to assess levels of hypoxia and acid-base balance
    • ARDS presents initially as hypoxemic respiratory failure with low PaO2 and respiratory alkalosis, later progressing into hypercapnic respiratory failure.
  • Inflammatory markers: High levels suggest immune dysregulation and progression to cytokine storm.
    • ↑ IL-6 and C-reactive protein in severe cases
    • ↑ procalcitonin in bacterial coinfection with pneumonia and/or sepsis
    • ↑ lactate in sepsis and septic shock
  • Hemostasis tests: 
    • Prolonged PT and PTT times
    • ↑ D-dimer in cardiac injury and septic shock (associated with high mortality)
  • Assessment of organ function: Abnormal findings may indicate multi-organ failure.
    • Creatinine, urea, and blood urea nitrogen used to assess renal function
    • Aspartate aminotransferase, alanine aminotransferase, gamma-glutamyl transferase, and bilirubin used to assess hepatic function
    • Cardiac enzymes (troponin and NT-proBNP) and electrocardiogram used to assess cardiac function
  • Chest X-ray and CT: severe infections may also present with the following:
    • Pleural thickening and effusion
    • Lymphadenopathy
    • Air bronchograms and atelectasis
    • Solid white consolidation

Serologic testing is not recommended for acute infections. Serology measures the host response to infection by the production of antibodies to SARS-CoV-2 and is an indirect measure of infection that is best utilized retrospectively. IgM responses are mainly nonspecific; specific IgG responses require weeks to develop; thus, serology detection plays an important role in surveillance, not in active case detection and management. It is vital in determining the immunity of healthcare workers as the outbreak progresses and the true mortality rate once the outbreak resolves.

Covid-19 Coronavirus disease 2019

The sensitivity and specificity of serologic tests are still uncertain, but preliminary studies have reported that seroconversion occurs after 7 days of symptomatic infection in 50% of cases and in 100% cases after 14 days.

These antibodies have also been shown to have neutralizing effects on SARS-CoV-2, explaining the current use of convalescent plasma as an investigational therapy. However, studies have shown that not all patients with COVID-19 develop neutralizing antibodies, and antibody response may be associated with the severity of the disease. One study showed that titers of SARS-CoV-2-specific neutralizing antibodies increase in parallel with the rise in IgG antibodies. The titers are low for the first 7–10 days after symptom onset, increase after 2–3 weeks, then decline gradually over several months after infection.

Differential Diagnoses

COVID-19InfluenzaCommon cold
Incubation period2–14 days1–4 days<3 days
FeverVery commonVery commonRare
Dry coughVery common (mild to severe)Very common (mild to severe)Common (usually mild, can be productive)
FatigueCommonVery CommonRare or mild
MyalgiaCommonVery CommonMild
SneezingSometimesRare or mildVery common
Nasal congestionRare or mildCommonVery common
HeadacheSometimesVery commonRare or mild
Sore throatSometimesSometimesVery common

Lecturio resources


No specific treatment for COVID-19 is currently available, and no pre- or post-exposure prophylaxis is currently being used or recommended. Healthcare professionals must always implement practices for infection prevention and control when dealing with a PUI or laboratory-confirmed COVID-19 case.

Covid-19 Coronavirus disease 2019

All healthcare personnel and patients with confirmed or possible SARS-CoV-2 infection should wear personal protective equipment (PPE). For further information, see the CDC’s “Infection Control Guidance for Healthcare Professionals about Coronavirus (COVID-19)” and “Using Personal Protective Equipment (PPE).”

According to clinical status and laboratory and radiological findings, COVID-19 patients can be grouped into the following illness categories:

  • Asymptomatic or presymptomatic infection: individuals who test positive for SARS-CoV-2 but have no symptoms
  • Mild case: individuals who present signs and symptoms without dyspnea or abnormal imaging
  • Moderate case: individuals who have evidence of lower respiratory disease due to signs and symptoms or radiological findings, but maintain a saturation of oxygen (SaO2) > 93% on room air at sea level
  • Severe case: individuals who have a respiratory rate > 30 breaths per minute, SaO2 ≤ 93% on room air at sea level, ratio of arterial partial pressure of oxygen to fraction of inspired oxygen (PaO2/FiO2) < 300, or infiltrates covering > 50% of the lungs
  • Critical case: individuals who have respiratory failure, septic shock, and/or multiple organ dysfunction
There are insufficient data to recommend the use of any antiviral or immunomodulatory therapy in patients with mild cases or asymptomatic or presymptomatic infections of COVID-19. It is recommended that these patients begin supportive at-home care. In the case of antipyretics, the use of ibuprofen is considered safe according to the WHO (March 17, 2020). In the outpatient setting, it is important to seek professional medical assistance if any of the following emergency warning signs develop:
  • Difficulty breathing or shortness of breath
  • Persistent pain or pressure in the chest
  • Confusion or inability to arouse
  • Cyanosis (bluish tint to lips or face)

Most patients with moderate-to-severe cases of COVID-19 require hospitalization, with critical cases requiring admission to an ICU. However, the decision to monitor a patient in the inpatient setting should be made on a case-by-case basis. Once hospitalized, supportive care and acute measures should be applied as necessary, and should include the following:

  • Breathing support is crucial in treating severe COVID-19 cases or any respiratory complication in order to alleviate and/or prevent respiratory distress, hypoxemia, or shock. The key elements include oxygen therapy by:
    • Nasal cannula or high-flow nasal oxygen
    • Prone mechanical ventilation
    • Extracorporeal membrane oxygenation (ECMO) for rescue in select cases
  • Empiric antimicrobials if sepsis or secondary pneumonia is suspected
  • Pharmacologic prophylaxis of venous thromboembolism:
    • Patients with COVID-19 who experience a thromboembolic event or are highly suspected to develop a thromboembolic disease should be managed with therapeutic doses of anticoagulant therapy as per the standard of care for patients without COVID-19.
    • A retrospective study showed reduced mortality in hospitalized patients with COVID-19 who received prophylactic anticoagulation.
    • Low-molecular-weight heparin or unfractionated heparin is preferred in hospitalized, critically ill patients.
  • Inhaled corticosteroids: continued use is recommended for patients who are already receiving steroids for another indication, such as asthma
  • Advanced oxygen therapy, ventilatory support, and conservative fluid management in the case of ARDS or respiratory failure
  • Fluid bolus and vasopressors in the case of septic shock
    • The COVID-19 Treatment Guidelines Panel recommends norepinephrine as the first-choice vasopressor.
  • Antifibrotic therapy may be beneficial both in the acute phase of the illness and in preventing long-term pulmonary fibrosis.
  • Clinical management of other comorbidities and nosocomial complication
  • Dexamethasone:
    • Preliminary evidence from a clinical trial has shown that it reduces death by one-third in ventilated patients and by one-fifth in patients receiving oxygen therapy only.
    • Thus, the use of low-dose dexamethasone (at a dose of 6 mg per day for up to 10 days) is now recommended for severely ill patients who are on supplemental oxygen or ventilatory support.
A distinction in treatment should be made between type L and type H patients. Type H patients should be treated as cases of severe ARDS. Their management, unlike those who are type L, should include higher positive end-expiratory pressure, if compatible with hemodynamics, prone positioning, and extracorporeal support.For the latest step-by-step management guidelines, see the “WHO interim guidance on clinical management of severe acute respiratory infection when novel coronavirus (nCoV) infection is suspected” or the “NIH COVID-19 Treatment Guidelines.”
Covid-19 Coronavirus disease 2019

The case fatality rate (CFR) of COVID-19 varies across different countries and age groups, with a global average crude rate of 2.33%; there have been 62,662,181 cumulative cases and 1,460,223 deaths to date, according to the “WHO Coronavirus Disease (COVID-19) Dashboard” on December 1, 2020. The CFR is not a biological constant, which is best estimated by the infection fatality rate, as it does not include infected people with mild or asymptomatic disease who were never tested.

The ongoing pandemic makes it difficult to determine an accurate mortality rate at this time. The rate is assumed to be lower than the current estimate due to many undetected cases (lack of widespread testing in many countries and asymptomatic individuals not seeking to be tested). 

Covid-19 Coronavirus disease 2019

Causes of death in COVID-19 patients include respiratory failure, multi-organ failure, and hypotensive shock.

Investigational therapies

Several clinical trials are currently being performed to further the development and research of antiviral drugs against SARS-CoV-2. However, there are no data available as of December 2020, to support the recommendation of any of the following investigational therapeutics for patients with confirmed or suspected COVID-19:

  • Remdesivir is reported to have in-vitro activity against SARS-CoV and MERS-CoV by entering nascent viral RNA chains and producing premature termination.
    • The Food and Drug Administration (FDA) issued an emergency use authorization for hospitalized children and adults with severe COVID-19.
    • The COVID-19 Treatment Guidelines Panel recommends the use of remdesivir for treatment of COVID-19 in any hospitalized patients who have a SpO2 ≤ 94% on room air, require supplemental oxygen, or are on mechanical ventilation or ECMO.
  • Chloroquine and hydroxychloroquine, widely used antimalarial drugs, are reported to block viral entry by inhibiting virus/cell fusion.
    • There are conflicting results from studies regarding their effectiveness in treatment; these results are even more confusing because of the differences in the timing of administration and their combination with other drugs. More prospective randomized studies are in progress.
    • The combined use of hydroxychloroquine and azithromycin, a macrolide antibiotic, was reported to reduce the detection of SARS-CoV-2 RNA in upper respiratory tract specimens. Caution is advised when administering these drugs in patients with underlying heart disorders as both are associated with QT prolongation and may lead to life-threatening arrhythmia or sudden death.
    • The FDA issued (and then withdrew) an emergency use authorization for hospitalized adolescents or adults with COVID-19 when participation in clinical trials is not feasible.
    • On July 30, 2020, Dr. Stephen Hahn, the FDA commissioner, declined to take a definitive stance on whether people should take hydroxychloroquine as a treatment for the coronavirus, instead noting that this decision should be made between a doctor and a patient.
  • Convalescent plasma with a SARS-CoV-2-specific antibody (IgG) has been reported, in preliminary studies, to improve clinical status.
  • RLF-100 (aviptadil) is a formulation of synthetic human vasoactive intestinal polypeptide (VIP) that is currently being tested in clinical trials. 
    • VIP targets the VPAC1 receptor of the alveolar type II cells in the lung and prevents apoptosis, increases surfactant production, blocks cytokines, lowers TNFα levels, and reduces cough and dyspnea.
    • In COVID-19 cases, VIP has suppressed the replication of the SARS-CoV-2 virus within the lung.
    • Emergency use in critically-ill COVID-19 patients in Switzerland who were ineligible for the clinical trials resulted in the rapid recovery and weaning from mechanical ventilation of 16 patients.
  • Lopinavir-ritonavir, a combined protease inhibitor usually used for HIV infection, was reported as having in-vitro inhibitory activity against SARS-CoV. However, no benefit was observed in hospitalized adult patients with severe Covid-19 in trials conducted in China.
  • Tocilizumab is an anti-IL-6 receptor agent used for rheumatoid arthritis. It is currently being investigated in patients with severe COVID-19 presenting with high IL-6 levels. 
  • Meplazumab is an anti-CD147 monoclonal antibody that has shown in-vitro inhibitory activity against SARS-CoV-2.
  • Camostat mesilate (CM), a TMPRSS2 inhibitor, is reported to block viral entry by inhibiting S protein priming.

For more information on international clinical trials, see the WHO website and

Lecturio resources


It is now a global recommendation that all individuals should help prevent the spread of COVID-19 infection. General recommendations include the following:

  • The use of face masks is now recommended for the general population.
    • Face masks help prevent the wearer from becoming infected and, just as importantly, prevent the wearer from transmitting the disease (also known as “source control”).
    • For healthcare personnel, PPE and National Institute for Occupational Safety and Health–approved N95 disposable filtering facepiece or higher-level respirators, such as a powered air-purifying respirator, are recommended when providing care for patients with suspected or confirmed COVID-19 due to higher exposure to infected individuals as well as aerosol-generating procedures (AGPs). AGPs include the following:
      • Open suctioning of airways
      • Sputum induction
      • Cardiopulmonary resuscitation
      • Endotracheal intubation and extubation
      • Non-invasive ventilation (e.g., BiPAP, CPAP)
      • Bronchoscopy
      • Manual ventilation
  • Caps: It is still unclear how long SARS-CoV-2 can survive on human hair, but healthcare personnel are encouraged to cover their hair with a disposable or surgical cap.
  • Home isolation and quarantine:
    • Avoid public/crowded areas whenever possible, particularly within closed buildings, to minimize the chance of exposure or transmission.
    • Before leaving and upon returning from travel, individuals should practice home isolation for 14 days, monitor the possible onset of symptoms, and be tested for COVID-19 if testing is available (especially if traveling to and from an area with a high infection rate). 
  • Respiratory hygiene: coughs and sneezes should be covered with a tissue or the inner elbow.
  • Washing hands regularly for at least 20 seconds with soap and water or with an alcohol-based hand sanitizer that contains at least 60% alcohol
  • Social distancing:
    • Maintain 1–2 meters (approximately 3–6 feet) distance from other people.
    • Avoid certain actions, such as forced expiration during yelling, singing, and exercise, as these can increase the volume and distance that respiratory droplets can travel.
  • Regular cleaning of all “high-touch” surfaces within the home or workplace (see the CDC’s “Cleaning and Disinfection for Households”)

Isolation and quarantine can be discontinued only after the following criteria have been met:

  • At-home and hospitalized symptomatic cases: 
    • Negative results of PCR testing obtained from at least 2 consecutive nasopharyngeal swab specimens collected ≥ 24 hours apart OR
    • At least 3 days have passed since the resolution of fever without the use of antipyretics and improvement in respiratory symptoms AND
    • At least 10 days have passed since the onset of symptoms
  • Asymptomatic cases:
    • Negative results of PCR testing obtained from at least 2 consecutive nasopharyngeal swab specimens collected ≥ 24 hours apart OR
    • At least 10 days have passed since the first positive COVID-19 diagnostic test  

For further information, see the CDC’s “Healthcare Infection Prevention and Control FAQs for COVID-19.”


There is no FDA-approved vaccine available to prevent COVID-19. Currently, there are 80+ candidate vaccines in preclinical evaluation, 70 vaccines in phases 1-3 of clinical evaluation, and 6 vaccines approved for early or limited use recognized by the World Health Organization (WHO). (For more information, see the WHO’s “Draft landscape of COVID-19 candidate vaccines.”)

Covid-19 Coronavirus disease 2019

Based on past experience, the European Medicines Agency’s estimates that it will take until the beginning of 2021 before an anti-COVID-19 vaccine is ready for approval and available in sufficient quantities for widespread use.

Currently, only 6 vaccines in the world have been approved for early or limited use. CanSino Biologics, a Chinese company, has developed an adenovirus-based vaccine called Ad5. After promising results from their Phase 1 and 2 trials in May and July, respectively, the Chinese military approved the vaccine as an “especially needed drug.” The Gamaleya Research Institute of Russia has been developing a vaccine, called Gam-COVID-Vac (and nicknamed Sputnik V), that is a combination of 2 adenoviruses engineered with a coronavirus gene. The Russian president announced on August 11, 2020, that Phase 1 and 2 results have been promising and that mass production has been approved. However, no results have been published under peer review.

The Bacille-Calmette-Guerin (BCG) vaccine, primarily used for the prevention of tuberculosis, is being evaluated for the prevention of COVID-19. Studies have reported that BCG immunization offers protection against various non-mycobacterial viruses, including herpes and influenza viruses. Clinical trials are underway to evaluate its efficiency against SARS-CoV-2.

Lecturio resources

Additional Resources: