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| Type of specimen used for COVID-19 testing | Stage of sample collection | Description |
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| Upper respiratory specimens: nasopharyngeal and oropharyngeal swabs | Early-stage infections (asymptomatic or mild cases) | Individual nasopharyngeal swabs are reported to be more reliable [49, 60, 78, 79]. Combining nasopharyngeal and oropharyngeal swabs increases sensitivity and reliability for detecting COVID-19 [79–82] |
| Lower respiratory specimens: sputum, endotracheal aspirate, bronchoalveolar lavage | Later in the course of the disease, the individuals with strong clinical suspicion of COVID-19 test negative with URT sampling [56, 60, 80, 83] | Sputum is not recommended because of an increase in aerosol transmission [84]. Requires consultation by a physician. Invasive sampling method |
Oral fluid collection methods
(i) Posterior oropharyngeal fluid/saliva (spitting/drooling)
(ii) Collection of oral fluid using pipette or sponges
(iii) Gargling with saline solutions | Individuals with clinical symptoms tested negative for URT | Less invasive and lower risk of exposure to other upon collection, when compared with the collection of URT specimens, therefore suitable for mass screening
But not recommended by WHO as the sole specimen type for routine clinical diagnosis [85–88] |
| Serum specimens | One collected in the acute phase and the other in the convalescent phase (2-4weeks) | Considered when nucleic acid amplification tests negative |
| Fecal specimens | Second week after the onset of symptoms | Considered when there is clinical suspicion of COVID-19, but URT and LRT are negative [89] |
| Postmortem specimens (postmortem swabs, needle biopsy, or tissue specimen) | Collected during autopsy | For pathological and microbiological testing [89–95] |
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