A definite diagnosis of Covid-19 requires viral testing, usually through PCR performed on upper (nasopharyngeal or oropharyngeal) or lower respiratory samples (sputum, bronchoalveolar lavage [BAL] fluid). Rates of positive PCR may be affected by stage of the disease and/or its severity.
Nasopharyngeal sample: This seems to be the most practical and readily available means of confirming Covid-19 diagnosis, with positive rates of ~75% during the first 2 weeks of illness in patients considered to have severe disease. For patients with mild Covid-19, a positive PCR rate of 72% has been reported during the 1st week, dropping to 54% during the 2nd week (1).
Oropharyngeal sample: Lower positive PCR rates have been observed with throat swabs, as low as ~30% in mild Covid-19 during the 2nd week of the illness and ~60% in severe disease during the first week of illness (2).
Sputum: Sputum may have the highest positive rates ranging from ~75% in mild disease during the second week of illness to ~90% during the 1st week of severe disease. The problem with sputum sampling is that less than one-third of patients with Covid-19 can provide a sample given the usually dry nature of their cough (1,4).
BAL fluid: In a limited number of patients with severe disease who had bronchoalveolar lavage sampling during the 2nd week of illness, 3 (25%) of 12 patients with positive PCR on BAL had negative upper respiratory samples (1). So in severe disease, the virus definitely prefers to replicate in the lower respiratory tract.
Potential explanations for a negative PCR include low viral titers and specimen handling. So, in patients suspected of having Covid-19 based on clinical/laboratory/radiograph grounds, a negative upper respiratory sample, particularly oropharyngeal source, should not rule out this disease.

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References

1. Yang Y, Yang M, Shen C, et al. Evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of 2019-nCoV infections. MedRxiv. 2020. DOI: http://doi.org/10.1101/2020.02.11.20021493
2. Ai T, Yang Z, Hou H, et al. Correlation of chest CT and RT-PCR testing in Coronavirus disease 2019 (COVID-19) in China: A report of 1014 cases. Radiology 2020. https://pubs.rsna.org/doi/10.1148/radiol.2020200642
3. Bai HX, Hsieh B, Xiong Z, et al. Performance of radiologists in differentiaging COVID-19 from viral pneumonia on chest CT. Radiology 2020. https://pubs.rsna.org/doi/10.1148/radiol.2020200823 
4. Huang C, Wang Y, Li X, et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 2020. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30183-5/fulltext
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