SARS-CoV-2

From IDWiki
Revision as of 13:25, 9 March 2022 by Aidan (talk | contribs)

Background

Microbiology

  • Coronavirus related to SARS-CoV
  • Virion consists of:
    • Spike glycoprotein (S), which appears to be an important virulence factor
      • Vaccines may target either the full protein or only its distal receptor binding domain
    • Membrane protein (M)
    • Nucleocapsid protein (N)
    • Hemagglutinin esterase (He)
    • Envelope protein (E)

Epidemiology

  • Transmitted mostly by respiratory droplets, with some amount transmission via aerosols and little to no transmission via contact
  • First cases detected Dec 2019 related to likely exposure in wet market in Wuhan, Hubei, China, and declared a pandemic in 2020
  • Secondary household attack rate of 12-17%
  • Possibility of animal reservoirs, including cats (possibly), dogs (unlikely), deer (probably)
    • Difficult to prove transmission to humans
    • Unlikely to contribute to household transmission, since human-to-human transmission is far more likely

Risk Factors for Mortality

Clinical Manifestations

Pregnancy

  • Please refer to a living systematic review on the topic
  • Slightly less reported fever and myalgias
  • Slightly more ICU admissions and mechanical ventilation
    • Risk factors included age, obesity, hypertension, and diabetes
  • With regards to the fetus, there were more preterm deliveries (6%) and more needed NICU admission (25%)

Severity

  • Mild: no oxygen
  • Moderate: supplemental oxygen
  • Severe: non-invasive mechanical ventilation
  • Critical: invasive mechanical ventilation

Bacterial Coinfection

Complications

Investigations

  • CT chest imaging may show:2
    • Typical appearance:, classic for COVID-19
      • Peripheral, bilateral ground-glass opacity with out without consolidation or visible intralobular lines (crazy paving)
      • Multifocal rounded GGO with or without consolidation or crazy paving
      • Reverse halo sign or other findings of organizing pneumonia (later finding)
    • Indeterminate appearance:
      • Multifocal, diffuse, perihilar, or unilateral GGO with or without consolidation lacking a specific distribution and are non-rounded or non-peripheral
      • Few very small GGO with a non-rounded and non-peripheral distribution
    • Atypical appearance, which suggests unlikely to be COVID-19:
      • Isolated lobar or segmental consolidation without GGO
      • Discrete small nodules (centrilobular, tree-in-bud)
      • Lung cavitation
      • Smooth interlobular septal thickening with pleural effusion

Diagnosis

  • PCR from NP swab
    • Highest sensitivity within 5 days of symptom onset, with decreasing sensitivity as the disease enters the immune-mediated phase
    • May be positive long after no longer infectious
  • Diagnostic accuracy of PCR by sample site (below) has a lot of heterogeneity among the studies
Sensitivity Specificity
Upper Respiratory Samples
Oral 56 99
Nasal 76 100
NP 97 100
Nasal 95 100
Saliva 85 100
Mid-turbinate 100 100
Upper Versus Lower Tract
Upper respiratory tract 57 100
Lower respiratory tract 81 100
Single Versus Repeat Testing
Single test 71 100
Repeat testing 100 100
  • Serology (IgM and IgG)
    • Total antibodies have poor sensitivity (51%) in first week, and increases to about 90% by week 3

Management

  • For patients no requiring supplemental oxygen, the focus is on supportive care
    • Remdesivir 200 mg IV once followed by 100 mg IV daily for 2 more days may be used within 7 days of symptom onset who have at least one risk factor for disease progression (age ≥60 years, obesity, or other medical conditions)3
    • Consideration of monoclonal antibodies such as casirivimab-imdevimab (Regeneron), depending on the variant
      • Use in patients who are anti-spike protein seronegative and within 9 days of symptom onset
      • May reduce hospitalization of high risk patients (hypertension, diabetes, chronic lung disease, congestive heart failure, of immunodeficiency) with ARR of 2 to 3%
    • Paxlovid may be considered for patients at high risk of progressing to severe disease, within 5 days of symptom onset
  • For patients requiring supplemental oxygen or with oxygen saturation less than 94%:
    • Dexamethasone 6 mg PO/IV daily for 10 days, which has a mortality benefit
    • Remdesivir 200 mg IV once on day one followed by 100 mg PO daily for 5-10 days, which has not been shown to have a mortality benefit
    • Tocilizumab indicated if progressing despite dexamethasone, still requiring oxygen and CRP ≥75 mg/L, per RECOVERY trial
      • ARR for 28-day mortality of about 4%
      • If tocilizumab is unavailable, then baricitinib 4 mg p.o. daily for 14 days or until hospital discharge
    • If unvaccinated/no prior infection, declining clinically, and within 9 days of symptom onset, casirivimab-imdevimab (Regeneron) 8000 mg IV once
  • Avoid hydroxychloroquine/chloroquine, lopinavir-ritonavir

Anticoagulation

  • A multiplatform RCT combined ATTACC, REMAP-CAP, and ACTIV-4a looked at therapeutic anticoagulation (compared to prophylactic)
    • Therapeutic anticoagulation with heparin derivatives, using the LMWH typical for the hospital at DVT/PE treatment doses
    • Duration 14 days, or until discharge if before 14 days
    • Helpful in moderately ill patients, regardless of D-dimer value
    • Potentially harmful in severely or critically ill patients

Strongyloidiasis

Prevention

Infection Prevention and Control

Healthcare Workers

  • Awaiting results
    • If symptomatic, HCWs should be off work
    • If asymptomatic, HCWs may return to work while awaiting results, depending on the reason for testing and the staffing needs
  • Positive but asymptomatic: in exceptional circumstances, may return to work early

Clearance

  • Non-test based (preferred)
    • Asymptomatic: isolate for 10 days from swab
    • Mild to moderate symptoms in immunocompetent person: 10 days from onset of symptoms, as long as afebrile (without antipyretics) and clinically improving
    • Severe (i.e. ICU-level care) or immunocompromised: 20 days from onset of symptoms, as long as afebrile (without antipyretics) and clinically improving
  • Test based (alternative): 2 negative swabs at least 24 hours apart (if still positive, repeat in 3 to 4 days), as long as afebrile and clinically improving

Further Reading

  • Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19): A Review. JAMA. doi: 10.1001/jama.2020.12839

Canadian Guidelines

References

  1. ^  Louise Lansbury, Benjamin Lim, Vadsala Baskaran, Wei Shen Lim. Co-infections in people with COVID-19: a systematic review and meta-analysis. Journal of Infection. 2020;81(2):266-275. doi:10.1016/j.jinf.2020.05.046.