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Subsections
COVID-19: Background, Pathophysiology, and Diagnostics

Infectious Diseases

COVID-19: Background, Pathophysiology, and Diagnostics

Background

  1. Definition
    • Formerly 2019-nCOV
    • Novel coronavirus (betacoronavirus) first identified in Wuhan, Hubei Province, China (View image)
      • The virus has been called Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV 2)
      • CDC named disease: Coronavirus Disease 2019 (COVID-19)
  2. Synopsis
    • Outbreak of pneumonia of unknown etiology in Wuhan City initially reported to WHO on December 31, 2019
    • Hundreds of confirmed cases and reports of cases rapidly rising worldwide
    • Supportive
      • Vaccines available
      • Health care providers
        • Obtain detailed travel history if patient evaluated with fever and acute respiratory illness
    • As of November 29, 2024
      • Variants of interest (VOIs)
        • BA.2.86
        • KP.3
      • Variants under monitoring (VUMs)
        • XEC

Pathophysiology

  1. Mechanism
    • Structure and cell entry
      • Coronavirus entry into host cells is mediated by the transmembrane spike (S) glycoprotein (homotrimers protruding from viral surface)
        • S comprises 2 functional subunits:
          • Binding to host cell receptor (S1 subunit)
          • Fusion of viral and cellular membranes (S2 subunit)
        • For many CoVs, S is cleaved at boundary between S1 and S2 subunits (remain non-covalently bound in prefusion conformation)
          • The distal S1 subunit comprises the receptor-binding domain(s)
            • Contributes to stabilization of prefusion state of membrane-anchored S2 subunit (contains the fusion machinery)
          • For all CoVs, S is further cleaved by host proteases at so-called S2′ site (immediately upstream of fusion peptide)
            • This cleavage has been proposed to activate protein for membrane fusion via extensive irreversible conformational changes
        • The Receptor binding domain is highly variable and may possibly account for the high mutagenicity of the virus
      • There is some evidence that SARS-CoV 2 glycoproteins also bind to heme groups in RBCs, leading to O2 dissociation (i.e., hypoxia without dyspnea)
    • Possible targets for treatment
      • SARS-CoV and several SARS-related coronaviruses (SARSr-CoV) interact directly with angiotensin-converting enzyme 2 (ACE2) to enter target cells
        • The SARS-CoV-2 SB engages human ACE2 (hACE2) with comparable affinity to SARS-CoV SB from viral isolates (i.e., binding with high affinity to hACE2)
        • Tight binding to hACE2 could partially explain the efficient transmission of SARS-CoV-2 in humans
        • SARS-CoV recognizes its entry receptor hACE2 at surface of type II pneumocytes using SB
          • ∼75% overall amino acid sequence identity with SARS-CoV-2 SB and 50% identity within their receptor-binding motifs (RBMs)
          • SARS-CoV S-elicited polyclonal antibody responses potently neutralize SARS-CoV-2 S-mediated entry into cells
        • Previous studies also showed host proteases cathepsin L and TMPRSS2 prime SARS-CoV S for membrane fusion through cleavage at S1/S2 and at the S2′ sites
      • The coronavirus S glycoprotein is surface-exposed and mediates entry into host cells (main target of neutralizing antibodies (Abs) upon infection/focus of therapeutic and vaccine design)
        • S trimers are extensively decorated with N-linked glycans
          • Important for proper folding and for modulating accessibility to host proteases and neutralizing Abs
    • Furin cleavage site at S1/S2 boundary of SARS-CoV-2 S (cleaved during biosynthesis) - a novel feature setting this virus apart from SARS-CoV and SARSr-CoVs
      • Furin-like proteases may expand SARS-CoV-2 cell and tissue tropism compared with SARS-CoV
      • It may also increase its transmissibility and/or alter its pathogenicity
    • Incubation: up to 2 weeks
      • Symptoms may develop 3-10 days
      • Disease course may take 2-3 weeks
    • Transmission: respiratory droplets and body fluids
      • Some evidence shows virus can be viable in the environment for hours
        • Studies seem to indicate virus is stable at cooler temperatures (40°F [4°C])
      • Viral shedding can occur from 8-37 days from time of symptom onset
    • For more genetic information: GISAID Initiative (https://www.gisaid.org/)
  2. Etiology/Risk Factors
    • Novel beta-coronavirus
      • Highly pathogenic zoonotic pathogens: SARS-CoV, MERS-CoV, and SARS-CoV-2, all belonging to the β-coronavirus genus
      • Low-pathogenic coronaviruses endemic in humans: HCoV-OC43, HCoV-HKU1, HCoV-NL63, HCoV-229E
    • Both SARS-CoV and SARS-CoV-2 are closely related
      • Originated in bats (most likely reservoir host for these two viruses)
        • Palm civets and racoon dogs are intermediate hosts for zoonotic transmission of SARS-CoV between bats and humans
        • However, SARS-CoV-2 intermediate host remains unknown
        • SARS-CoV-2 is most closely related to the bat SARSr-CoV RaTG13, with which it forms a distinct lineage from other SARSr-CoVs, and that their S glycoproteins share 97% amino acid sequence identity
    • There are recurrent spillovers of coronaviruses in humans along with detection of numerous coronaviruses in bats, including many SARS-related coronaviruses (SARSr-CoVs)
      • Suggests that future zoonotic transmission events may continue
    • Travel to endemic areas (Wuhan City, Hubei Province) within the last few weeks/months
      • Thailand and Japan have confirmed additional cases in travelers from Wuhan, China
    • Modes of transmission
      • Close-range contact via respiratory particles
        • Coughing
        • Sneezing
        • Talking
        • Inhaled/makes direct contact with mucous membranes
  3. Epidemiology
    • Incidence/Prevalence
      • Emerging disease
      • WHO: Presumed to have originated in Wuhan, China
      • First case in USA announced January 21, 2020
      • > 770,000,000 confirmed cases worldwide
    • Mortality/Morbidity
      • > 6,900,000 deaths worldwide
      • USA
        • 6,502,997 hospitalizations
        • 1,155,145 deaths
      • 2023 USA
        • 916,300 people hospitalized
        • 75,5000 deaths
      • Higher risk of mortality amongst older adults, especially with underlying illnesses/immunocompromised (e.g., DM, cardiovascular disease, etc.)
      • Pneumonia is a significant risk for mortality
        • See the MuLBSTA Score
        • Specific for Viral pneumonia similar to COVID-19 induced, but may not yet be valid for COVID-19 patients (use with caution)

Diagnostics

  1. History/Symptoms
    • Most common
      • Fever/chills
      • Cough
      • SOB, dyspnea
      • Fatigue
      • Muscle, body aches
      • Headache
      • Sore throat
      • New loss of taste or smell
      • Congestion or runny nose
      • Nausea or vomiting
      • Diarrhea
    • Emergency warning symptoms
      • Shortness of breath
      • Persistent pain or pressure in the chest
      • New confusion or inability to arouse
      • Bluish lips or face
  2. Physical Exam/Signs
    • Asymptomatic Infections
      • May still have objective clinical abnormalities (e.g., typical ground-glass opacities, patchy shadowing, atypical imaging abnormalities)
    • Mild Illness
      • In uncomplicated upper respiratory tract viral infection
      • May have no signs during early infection
      • Rarely: diarrhea, nausea, and vomiting
      • No or mild pneumonia
      • Elderly and immunosuppressed may present with atypical signs/symptoms
      • Signs/Symptoms due to physiologic adaptations of pregnancy or adverse pregnancy events (e.g. dyspnea, fever, GI-symptoms, or fatigue) may overlap with COVID-19 signs/symptoms
    • Pneumonia
      • Adult
        • Imaging indicating pneumonia but no signs of severe pneumonia AND NO need for supplemental oxygen
      • Children
        • Non-severe pneumonia in a child with cough/difficulty breathing AND tachypnea
          • RR- < 2 months: ≥ 60; 2–11 months: ≥ 50; 1–5 years: ≥ 40
        • NO signs of severe pneumonia
      • Severe pneumonia
        • Adolescents or adults- fever or suspected respiratory infection in plus one of the following:
          • Respiratory rate > 30 breaths/min
          • Severe respiratory distress OR SpO2 ≤ 93% on room air
        • Children- cough or difficulty in breathing, plus at least one of the following:
          • Central cyanosis or SpO2 < 90%
          • Severe respiratory distress (e.g. grunting, very severe chest indrawing)
          • Signs of pneumonia with a general danger sign: inability to breastfeed or drink, lethargy or unconsciousness, or convulsions
          • Other signs: chest indrawing, tachypnea (in breaths/min): < 2 months: ≥ 60; 2–11 months: ≥ 50; 1–5 years: ≥ 40
          • While the diagnosis is made by clinical means, chest imaging can help identify/exclude pulmonary complications
    • Acute Respiratory Distress Syndrome
      • Onset: within 1 week of a known clinical insult or new/worsening respiratory symptoms
      • Chest imaging (radiograph, CT scan, or lung ultrasound): bilateral opacities, lobar or lung collapse, nodules
      • Origin of pulmonary infiltrates and respiratory failure should not completely be explained by cardiac failure or fluid overload
      • Oxygenation impairment in adults:
        • Mild ARDS: 200 mmHg < PaO2/FiO2 ≤ 300 mmHg (with PEEP or CPAP ≥ 5 cmH2O, or non-ventilated)
        • Moderate ARDS: 100 mmHg < PaO2/FiO2 ≤ 200 mmHg (with PEEP ≥ 5 cmH2O, or non-ventilated)
        • Severe ARDS: PaO2/FiO2 ≤ 100 mmHg (with PEEP ≥ 5 cmH2O, or non-ventilated)
        • When PaO2 is not available, SpO2/FiO2 ≤ 315 suggests ARDS (including in non-ventilated patients)
      • Oxygenation impairment in children:
        • NOTE: OI = Oxygenation Index and OSI = Oxygenation Index using SpO2
        • Use PaO2-based metric when available
        • If PaO2 not available, wean FiO2 to maintain SpO2 ≤ 97% to calculate OSI or SpO2/FiO2 ratio:
          • Bilevel (NIV or CPAP) ≥ 5 cmH2O via full face mask: PaO2/FiO2 ≤ 300 mmHg or SpO2/FiO2 ≤ 264
          • Mild ARDS (invasively ventilated): 4 ≤ OI < 8 or 5 ≤ OSI < 7.5
          • Moderate ARDS (invasively ventilated): 8 ≤ OI < 16 or 7.5 ≤ OSI < 12.3
          • Severe ARDS (invasively ventilated): OI ≥ 16 or OSI ≥ 12.3
    • Sepsis
      • Adults
        • Life-threatening multi-organ dysfunction due to proven infection:
          • Altered mental status
          • Difficult/fast breathing
          • Low oxygen saturation
          • Reduced urine output
          • Tachycardia, hypotension, weak pulse, cold extremities, skin mottling, or laboratory evidence of coagulopathy
          • Thrombocytopenia
          • Acidosis, high lactate, or hyperbilirubinemia
      • Children
        • Suspected/proven infection AND
        • ≥ 2 aged based systemic inflammatory response syndrome criteria, of which one must be abnormal temperature or white blood cell count
    • Septic shock
      • Adults
        • Persistent hypotension despite volume resuscitation,
        • Need of vasopressors to maintain MAP ≥ 65 mmHg and
          serum lactate level > 2 mmol/
      • Children
        • Any hypotension OR two or three of the following:
          • Altered mental state
          • Tachycardia or bradycardia (HR < 90 bpm or > 160 bpm in infants and HR < 70 bpm or > 150 bpm in children)
          • Prolonged capillary refill (> 2 sec) or weak pulse tachypnea
          • Mottled or cool skin or petechial or purpuric rash;
          • Increased lactate
          • Oliguria
          • Hyperthermia or hypothermia
  3. Labs/Tests
    • There may be available FDA-approved bedside tests
    • Common labs/tests profile for severe cases/poor outcomes (may be anecdotal from multiple sources)
      • May be hypoxic +/- dyspnea
      • May have late onset (> 5 days) cytokine storm leading to ARDS in severe cases (ARDS is leading cause of mortality); the following are elevated
        • IL-6, IL-2, IL-7
        • Granulocyte-colony stimulating factor
        • Interferon-γ inducible protein 10
        • Monocyte chemoattractant protein 1
        • Macrophage inflammatory protein 1-α
        • Tumor necrosis factor-α
      • Secondary hemophagocytic lymphohistiocytosis (sHLH)
        • Fulminant and fatal hypercytokinemia with multiorgan failure
          • Unremitting fever, cytopenias, hyperferritinemia, and elevated CRP
          • Elevated LFT, CPK, LDH, D-dimer
          • ANC:Absolute lymphocyte count > 3.5 may predict poor outcome
        • See the HScore calculator
    • Testing Criteria
      • Consider COVID-19 testing if
        • New onset fever and/or respiratory tract symptoms (e.g., cough, dyspnea)
        • Severe lower respiratory tract illness without clear etiology
        • Other symptoms: myalgias, diarrhea, and smell or taste changes etc.
        • May present with atypical signs/symptoms (clinical judgement)
      • Significant likelihood of COVID-19 if
        • Resides/travels to endemic areas with widespread transmission or
        • Close contact with confirmed/suspected COVID-19 patient within 14 days
          • Close contact defined as
            • Being within approximately 6 ft [2 m], or
            • Within the room/care area for a prolonged period of time without recommended personal protective equipment (PPE)
          • Close contact can include:
            • Caring for, living with, visiting, or sharing a healthcare waiting area or room with confirmed infected patient, or
            • Having direct contact with infectious secretions while not wearing recommended PPE
      • Non-emergent suspected COVID-19 should call their PCP before going to a health care facility
    • Guidance for Testing Priority (due to limitations of test availability)
      • CDC Guidance
        • PRIORITY 1
          • Ensure optimal care options for hospitalized patients, decrease risk for nosocomial spread, maintain integrity of healthcare system
          • Health care facility workers, workers in crowded living settings, and first responders with symptoms
          • Residents in long-term care facilities or other crowded living conditions with symptoms (e.g., prisons and shelters)
          • Individuals identified/contacted via public health cluster and selected contact investigations
        • PRIORITY 2: Persons identified by public health officials or clinicians as high priority
          • Symptoms of potential COVID-19
            • Fever, cough, shortness of breath, chills, myalgia, new loss of taste/smell, vomiting/diarrhea and/or sore throat
          • Without symptoms who are from racial and ethnic minority groups disproportionately affected by adverse COVID-19 outcomes
            • African Americans
            • Hispanics and Latinos
            • Some American Indian tribes (e.g., Navajo Nation)
          • Without symptoms but prioritized by health departments or clinicians, including but not limited to:
            • Public health monitoring
            • Sentinel surveillance
            • Comorbidity or disability
            • Residency in a congregate housing setting (e.g., homeless shelter or long-term care facility)
            • Screening of other asymptomatic individuals according to state and local plans
    • IDSA Guidance
      • SARS-CoV-2 NAAT recommended in symptomatic individuals suspected of having COVID-19
        • Strong recommendation, moderate certainty evidence
      • Symptomatic individuals suspected of having COVID-19
        • Suggest collecting and testing swab specimens from either
          • Nasopharynx, anterior nares, oropharynx, or mid-turbinate regions; saliva or mouth gargle
          • Conditional recommendation, low certainty evidence
      • Symptomatic individuals suspected of having COVID-19
        • Anterior nasal (AN) and MT swab specimens may be collected for SARS-CoV-2 RNA testing by
          • Either patients or healthcare providers
            • Conditional recommendation, moderate certainty evidence
      • Use of either rapid or standard lab-based NAATs in symptomatic individuals suspected of
        • Having COVID-19
          • Conditional recommendation, moderate certainty of evidence
      • Performing a single NAAT and not repeating testing routinely in symptomatic or
        • Asymptomatic individuals suspected of having COVID-19 whose initial NAAT result is negative
          • Conditional recommendation, very low certainty of evidence
      • For individuals who have clinical or epidemiologic reasons that might make testing desirable
        • Suggests SARS-CoV-2 RNA testing in asymptomatic individuals
          • Who are either known or suspected to have been exposed to COVID-19
            • Conditional recommendation, moderate certainty evidence
        • Suggests using either rapid or standard laboratory-based NAATs in asymptomatic individuals with known exposure to SARS-CoV-2 infection
      • SARS-CoV-2 NAAT is not suggested for routine use in
        • Asymptomatic individuals w/o known exposure to COVID-19
          • Who are being hospitalized
            • Conditional recommendation, very low certainty evidence
        • Who are undergoing a medical or surgical procedure
          • Conditional recommendation, very low certainty evidence
      • NAAT is suggested not to be repeated for pts w/ COVID-19 to guide release from isolation
        • Conditional Recommendation, very low certainty evidence
      • Suggests neither for nor against home testing for SARS-CoV-2
        • Evidence gap
    • Microbiologic Testing
  4. Imaging
    • ACR Recommends Chest Xray and CT for suspected COVID-19 Infection
      • Chest CT has a high sensitivity for diagnosis of COVID-19 (consider as primary tool for the current COVID-19 detection)
      • Sensitivity: 97% (95%CI, 95-98%, 580/601 patients) based on positive RT-PCR results
        • Negative RT-PCR results: 75% (308/413) had positive chest CT findings
          • Of 308, 48% were considered as highly likely cases, with 33% as probable cases
    • Chest X-ray (View image)
      • May be normal or pneumonia-like (e.g., infiltrates, airspace opacities, lobar/lobular consolidation, etc.)
      • CXR of 35 yo male with positive COVID-19 (View image)
        • Patient illness day 10, hospital day 6
        • Image shows stable streaky opacities in lung bases (likely atypical pneumonia)
          • Opacities steadily increased in density over time on serial CXR
    • CT (View image)
      • 75% of cases have presented with bilateral pneumonia
      • Typical findings:
        • Ground-glass opacities in all hospitalized patients
        • Inter-/intra-lobular septal thickening
        • Air space consolidation
        • Vascular enlargement in the lesion
        • Traction bronchiectasis
      • Atypical findings:
        • Mediastinal lymphadenopathy
        • Pleural effusions
          • May occur as a complication of COVID-19
        • Multiple tiny pulmonary nodules
          • Unlike many other viral pneumonias
      • Progression CT: 29 yo male positive for COVID-19 with fever for 6 days (View image)
        • (A) normal chest CT: axial and coronal planes at onset
        • (B) chest CT: axial and coronal planes- minimal ground-glass opacities in bilateral lower lung lobes
        • (C) chest CT: axial and coronal planes- increased ground-glass opacities
        • (D) chest CT: axial and coronal planes- progression of pneumonia with mixed ground-glass opacities and linear opacities in subpleural area
        • (E) chest CT: axial and coronal planes- absorption of both ground-glass opacities and organizing pneumonia
    • Electron microscopy (View image)
      • Allows gross visualization of the virus
      • Color electron microscopy (View image)
  5. Other Tests/Criteria
    • CDC has developed a real time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR) test that can diagnose 2019-nCoV
    • Criteria to Guide Evaluation
      • Fever AND symptoms of lower respiratory illness and in the last 14 days before symptom onset
        • History of travel from Wuhan City, China, or
        • Close contact with an ill person under investigation for COVID-19
      • Fever or symptoms of lower respiratory illness and in the last 14 days before symptom onset
        • Close contact with an ill lab-confirmed COVID-19 patient
    • Fever may not be present (i.e., very young, elderly, immunosuppressed, or taking certain fever-lowering medications)
      • Clinical judgment should be used to guide testing of patients in such situations
    • Close contact with a person who is under investigation for COVID-19
      • Close contact is defined as
        • Being within approximately 6 ft [2 m], or
        • Within the room or care area for a prolonged period of time while not wearing recommended personal protective equipment (PPE)
          • For example: gowns, gloves, NIOSH-certified disposable N95 respirator, eye protection
      • Close contact can include:
        • Caring for, living with, visiting, or sharing a healthcare waiting area or room with confirmed infected patient, or
        • Having direct contact with infectious secretions while not wearing recommended PPE (e.g., being coughed on)
    • Multisystem inflammatory syndrome in children (MIS-C) criteria:
      • Hospitalization, fever > 24 hrs
      • Lab evidence of inflammation, signs of > 2 organs involved, or epidemiologic association with SARS-COV-2 infection
      • Features of Kawasaki disease or Toxic shock syndrome
      • Postinfectious inflammatory syndrome (fever, tachycardia, and gastrointestinal symptoms with systemic inflammatory signs)
      • Report to CDC
    • COVID-19 breath test
      • InspectIR COVID-19 Breathalyzer test
        • Provides COVID result in 3 minutes
        • 91.2% sensitivity and 99.3% specificity
        • Negative predictive value 99.6%
        • Uses has chromatography gas mass-spectrometry (GC-MS0 to separate and identify
          • Chemical admixtures and rapidly detect 5 Volatile Organic Compounds (VOCs)
          • Assoc/ w/ SARS-CoV-2 infection in exhaled breath
  6. Differential Diagnosis

Related Topics

References

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  11. Gautret, et al. Hydroxychloroquine and azithromycin as a treatment of COVID‐19: results of an open‐label non‐randomized clinical trial. International Journal of Antimicrobial Agents. In Press March 17, 2020
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Contributor(s)

  1. Wedro, Benjamin, MD
  2. Ho, Nghia, MD
  3. Cherian, Geo, MD
  4. Singh, Ajaydeep, MD

Updated/Reviewed: November 2024