Most sore throats are caused by colds, the flu, coxsackie virus or mono (mononucleosis). Bacteria that can cause pharyngitis in some cases: 1  Strep throat is caused by group A streptococcus.  Less commonly, bacterial diseases such as gonorrhea and chlamydia can cause sore throat.
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For testing, clinicians should: 1  Obtain a nasopharyngeal swab from the patient; 2  Place the swab in a viral transport medium; 3  Refrigerate the specimen (do not freeze); and then. 4  Contact their state or local health department to facilitate transport and a timely diagnosis at a state public health laboratory.