COVID-19 was first recognized in 2019. Since then, it has undergone numerous gene mutations resulting in variants of concern, including Omicron, which was first reported in the United States in December 2021. Omicron has greater transmissibility and immune evasion than previous variants and the ancestral strain, regardless of an individual's vaccination status. Further observation is needed to fully determine hospitalization and mortality rates; however, despite its apparent lower risk for severe disease and fatality, the overall risk for infection remains high.
Patients with COVID-19 caused by the Omicron variant may present with fever, chills, fatigue, headache, anosmia, nasal congestion or rhinorrhea, pharyngitis, cough, dyspnea, or myalgia. Occasionally, patients have gastrointestinal involvement, including dysgeusia, diarrhea, nausea, vomiting, abdominal pain, and diminished appetite. Although some COVID-19 variants are associated with prolonged viral shedding in the gastrointestinal tract and the virus is detectable in waste water, whether fecal-oral transmission is a significant mode of transmission remains unclear.
Symptom severity varies, ranging from asymptomatic to mild, moderate, severe, or critical illness. Patients with increased viral load or underlying comorbidities, such as diabetes, cardiovascular disease, obesity, or immunosuppression, are at increased risk for worse disease or delayed recovery. COVID-19 is also linked to leukopenia or leukocytosis with lymphopenia, as well as elevation of inflammatory markers, such as ferritin, lactate dehydrogenase, and C-reactive protein. Furthermore, owing to liver involvement, liver enzyme levels may also be elevated.
In patients with suspected COVID-19, rapid antigen detection tests (RADTs) and real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) are the most common diagnostic tests. According to the Centers for Disease Control and Prevention guidelines, suspicion of COVID-19 is low in persons without close contact exposure within the past 14 days, who have full vaccination status, or who have had COVID-19 within the past 3 months. Suspicion of COVID-19 is high in persons with known close contact exposure within the past 14 days, an incomplete vaccination series, and an absence of COVID-19 infection within the past 3 months.  The initial COVID-19 test for both asymptomatic and symptomatic patients in the community setting is RADT, with rRT-PCR recommended as a follow-up confirmatory test if suspicion of COVID-19 remains high.
COVID-19 RADT is the most common and commercially available test and is typically performed with nasal, nasopharyngeal, or saliva specimens in point-of-care settings. It can detect viral antigens in high viral loads of active COVID-19 and can allow for faster diagnosis, isolation, and therapy initiation.[4,5]
COVID-19 rRT-PCR is the criterion standard test for COVID-19 diagnosis and is typically performed with nasal and nasopharyngeal specimens. It uses nucleic acid amplification testing to detect and measure viral RNA despite viral load and can complete whole-genome sequencing to determine variant lineage.[5,6]
The diagnostic accuracy of RADTs for the detection of COVID-19 variants is concerning, given the emergence of gene-sequencing mutations. Most notably, false-negative results and decreased sensitivity for the detection of vaccine-breakthrough Omicron variant have been investigated. In fully vaccinated, COVID-19–naive patients with new-onset symptoms, the specificity (100%) and sensitivity (81.8%) of RADTs are dependent on a greater viral load and specimen collection within 0-1 days of symptom onset.[5,6] Furthermore, evidence suggests that RADTs have a significant increase in sensitivity with increasing viral loads.Oral cheek (9% sensitivity) and tonsillar (46.9% sensitivity) specimens have been reported to be less reliable than nasal swab (85.7% sensitivity) specimens. Of note, RADTs manufactured by different companies have different sensitivities and results. Therefore, further studies are needed to compare diagnostic accuracy among these tests.
rRT-PCR consistently produces better viral load measurements and is more sensitive than RADT, despite the time of specimen collection. Nasopharyngeal swab remains the ideal specimen collection site for COVID-19 detection. In the patient in this case, who had gastrointestinal manifestations of COVID-19, rRT-PCR is the recommended test; it may detect viral particles in feces despite a negative result in a nasopharyngeal specimen from the respiratory tract.
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