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Understanding the most commonly billed diagnoses in primary care

Acute pharyngitis

Rogers, Julia DNP, RN, CNS, FNP-BC; Eastland, Taryn PhD, RN

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doi: 10.1097/
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This is the final article in a 12-part series on the most commonly billed diagnoses in primary care. The top 12 billable diagnoses were retrieved from compiling information obtained from the Centers for Medicare and Medicaid Services (CMS) and the CDC.1,2 The information is based on the best-available evidence. This article will focus on acute pharyngitis in adults.

Sore throat is one of the most common complaints presented by patients in an outpatient primary care setting.2-4 The etiology of infectious cases stems from invasion of a pathogen that causes inflammation of the tonsils and pharynx and is termed acute pharyngitis.3-5 In the US, an estimated 15 million annual healthcare visits are attributable to acute pharyngitis; however, the incidence may be underestimated because many individuals do not seek care.5,6 Adult cases are responsible for more than 7 million of those office visits.7 The financial burden is substantial, with total associative costs being more than $500 million per year.7,8

Acute pharyngitis can be caused by viral, bacterial, or sexually transmitted infections (STIs). Viral etiologies include the rhinovirus, adenovirus, and Epstein-Barr virus (EBV); the latter is the cause of most cases of infectious mononucleosis.9,10 The most common bacterial cause of acute pharyngitis is Streptococcus pyogenes, or group A streptococcus (GAS), which accounts for approximately 5% to 15% of adult cases.3,5,6,8 STIs such as herpes simplex virus (HSV) and gonorrhea can cause acute pharyngitis among those with high-risk behaviors.10 Other less common causes of acute pharyngitis include allergies, trauma, cancer, gastroesophageal reflux disease, and certain toxins.11


The nasopharynx and oropharynx constitute the first line of defense for most infectious agents. The nasopharynx is lined with hair and pseudostratified columnar epithelium to trap unwanted organisms. The shape of the nasopharynx also aids in the defense. Inhaled air can pass through the downward angle of the nasopharynx. However, large particles have difficulty making the 90-degree turn and get stuck to the mucosa near the tonsils.12,13 The adenoids and tonsils contain immunologic cells that attack undesired pathogens.12,13 Normal microbiome are found in different parts of the body, including the oropharynx. These microbes consist of bacteria, viruses, and fungi. While these microorganisms are potentially pathogenic, they may not necessarily cause disease. However, there is opportunity for these organisms to invade and cause disease when protective barriers or defensive mechanisms are weakened.12,13

The progression of an acute pharyngitis infection includes colonization, invasion, multiplication, and dissemination of pathogenic microorganisms. Transfer of microorganisms can occur through contact, droplet, or airborne transmission. Respiratory transmission occurs via several mechanisms. Coughing, sneezing, and breathing of an infected individual can produce airborne droplets that create a mist, which can be inhaled from the air, transmitting microorganisms capable of causing pharyngitis.12,13 STIs are mostly transmitted by sexual contact.

Prostaglandins, which are inflammatory mediators, play a key role in the generation of the inflammatory response. Their biosynthesis is significantly increased in inflamed tissue and they contribute to the development of the cardinal signs of acute pharyngitis. Prostaglandin E2 is released in response to inflammation and acts on the brain to induce fever. Additionally, bradykinins are potent stimulators of pain nerve endings and play an important role in the pathogenesis of an inflamed sore throat.12,13

Viral pharyngitis. Viruses are less complex microorganisms than bacteria and do not possess any of the metabolic organelles found in prokaryotes.12,13 The basic viral structure consists of nucleic acid protected by the capsid, a protein shell. The viral life cycle involves attaching to the target cell, penetrating, uncoating, replication, assembly, and release.12,13 As part of their replication, viral pathogens damage infected cells. The most common viral pathogens associated with acute pharyngitis are the rhinovirus and adenovirus. A rhinovirus enters through the nares and causes an inflammatory response producing edema and erythema of the nasal cavity and pharynx, which can lead to subsequent obstruction. Adenoviruses differ from rhinoviruses in that they directly invade the pharyngeal mucosa. However, an adenovirus can cause a similar inflammatory response, causing hyperemia of the pharynx. The mild symptoms associated with viral infections, such as fever and malaise, are caused by this inflammatory response.12,13

Bacterial pharyngitis. Bacteria are prokaryotic unicellular microorganisms with no nuclei, mitochondria, or membrane-bound organelles.12,13 Many bacteria have specialized surface structures that contribute to the structural integrity of biofilms and provide adherence to cells and tissue during invasion. The flagella, which allow the bacteria to move, express adhesins allowing GAS bacterial adherence.12,13S. pyogenes (GAS) is a highly adapted pathogen, with humans as its only known biological host.14,15 It is the most common bacterial pathogen of pharyngitis and tends to colonize the oropharyngeal mucosal epithelium of the upper respiratory tract and the superficial layers of the epidermis.5,6,15 Once colonization is established, the organism can cause symptomatic pharyngitis, with or without tonsillitis.15 Oropharyngeal infection can be cleared by a protective antibody produced by the host in response to infection.15

Alternatively, an infection can arise in an individual that remains asymptomatic, yet a specific immune response is directed to antigens of the infecting organism.15 It is also possible for the bacteria to reside within the nasopharynx with an absence of host immunologic response to the organism.14,15 This can contribute to adults being carriers of GAS. The carrier state can persist for weeks or months, during which the organism remains capable of transmission to a new host. A contributing factor in persistent infection of a GAS carrier includes the bacterial communities that arise from microcolony and biofilm formation.15

Sexually transmitted pharyngitis. Two of the most common pathogens related to sexually transmitted pharyngitis are HSV and gonorrhea. HSV pharyngitis is caused by HSV type 1 or 2. Gonococcal pharyngitis is caused by the bacterium Neisseria gonorrhoeae, which is a Gram-negative diplococcus.10 HSV and gonococcal pharyngitis can occur after oral sexual contact with an infected partner.10,12,13

History, physical exam, and diagnosis

It is important to obtain and document a thorough history of a patient presenting with symptoms of a sore throat to differentiate between viral, bacterial, and sexually transmitted etiologies. Most patients with acute pharyngitis of any cause present with similar symptoms, including a sore throat that worsens when swallowing, neck pain, headache, and fatigue.8 It is essential for the NP to differentiate the cause of acute pharyngitis because the management varies significantly.

During the focused history, documentation should include the onset of symptoms, precipitating events, location, intensity and quality of pain, progression, alleviating and aggravating factors, previous episodes, and associated symptoms. The NP should document allergies, ill contacts, autoimmune diseases, and medical, social, and family history including any accounts of rheumatic fever. The patient evaluation for acute pharyngitis should include a sexual history. A record should be made regarding the patient's past and current history of STIs, gender and number of partners, and use of protection. High-risk behaviors, such as illicit drug use, should also be evaluated.10 The NP can rarely distinguish the cause of acute pharyngitis based on the clinical symptoms alone. It is necessary to conduct a thorough physical exam (PE).

The PE should include documentation of weight and vital signs, as well as any irregular assessment findings of the head, eyes, ears, nose, and throat (HEENT), respiratory, gastrointestinal, and integumentary systems. As part of the HEENT exam, the color of the mucosa, amount and color of exudates, and presence of oral lesions should be specified in the patient's chart. A neck exam identifies cervical adenopathy, such as swelling and tenderness.5,6,8 The NP should assess the quality of breath sounds in all lung fields, documenting key findings such as absent breath sounds, crackles, wheezes, and rhonchi. An abdominal exam is performed to assess for hepatosplenomegaly, especially if the patient complains of abdominal pain. (Refer to the January 2021 abdominal pain article in this series for further information.) A thorough integumentary exam should be completed, recording any rash that may be associated with acute pharyngitis.5,6,8

During the PE, the NP should be alert for any red flags that could signal a potentially serious or life-threatening illness. Signs or symptoms of potentially progressive complications or other serious conditions may include: bilateral throat soreness, neck stiffness, trismus, uvular deviation, drooling, inability to swallow liquids, voice changes, stridor, and submental lymphadenopathy. Some pathologies suspected with red flags include peritonsillar abscess, retropharyngeal abscess, epiglottitis, Kawasaki disease, and airway obstruction.8 If the patient presents with red flags, the NP should refer to the ED for urgent airway management and care.

Patients with acute pharyngitis caused by a virus typically have signs and symptoms consistent with an upper respiratory tract infection. Viral clinical manifestations include conjunctivitis, coryza, cough, diarrhea, hoarseness, discrete oral ulcers, and viral exanthema.5,6,8 EBV causes most infectious mononucleosis cases, and its symptoms may be confused with those of GAS infection because of the patchy pharyngeal exudates and palatal petechiae.5,8 In contrast with other forms of acute pharyngitis, symptoms caused by acute EBV infection are prolonged, often lasting 2 to 3 weeks. Infectious mononucleosis is more common in individuals 10 to 30 years of age.9 Additional distinguishing features may include splenomegaly, atypical lymphocytosis, fatigue, headaches, and fever.9

GAS pharyngitis should be suspected in patients with an acute onset of sore throat predominately in winter or early spring with complaints of fever, odynophagia, absent cough, headache, nausea, vomiting, abdominal pain, and possible exposure to the illness.5,6,8 PE findings that support the diagnosis include tonsillar inflammation and exudates, palatal petechiae, anterior cervical adenitis, and scarlatiniform rash.5,8 GAS colonization is commonly seen in adults over age 30 years.9 It should be noted that up to 30% of patients are colonized with GAS; therefore, even though diagnostics may signal the presence of GAS, the patient should be suspected of having a secondary viral or STI etiology if there are no clinical symptoms of GAS present.9

It is important for the NP to rule out STIs as the cause of acute pharyngitis in any patient with high-risk factors. While many patients with pharyngitis caused by HSV or N. gonorrheae are asymptomatic, some may complain of a sore throat or pharyngeal ulcerations.10 Local symptoms can remain mild and unnoticed; however, the presence of painful oral lesions is one of the most distinctive characteristics of HSV.10 Other assessment findings in STI pharyngitis may include an erythematous throat with enlarged tonsils and mucopurulent exudate.10


The decision to perform diagnostic testing on patients presenting with acute pharyngitis should be based on the clinical and epidemiologic characteristics of the illness.5 Testing in adults is only recommended for patients whose clinical and epidemiologic features do not reliably discriminate between viral or bacterial infection and for patients suspected of STI etiology.5 For adults whose signs and symptoms do not differentiate the cause, the use of the rapid antigen detection test (RADT) for GAS pharyngitis can prevent unnecessary prescribing of antibiotics.7 The diagnosis of GAS can be quickly established through the RADT, which involves swabbing the individual's throat.5 The RADT has a sensitivity between 70% and 96% and specificity between 95% and 96% in adults.5,7 It is not necessary to have a backup throat culture for a positive result, as the RADT is highly specific. In adults, a backup throat culture is also unnecessary for negative RADTs due to the decreased incidence of GAS in adults and low risk of rheumatic fever in adults with acute pharyngitis.5,7,16 Diagnostic testing of asymptomatic household contacts is also not recommended.5

Multiple clinical prediction rules have been developed to aid in the diagnosis of GAS pharyngitis. Scoring systems attempt to use clinical and epidemiologic data to assign a probability that acute pharyngitis is caused by GAS.5,8 The most widely used criteria are the Centor score and modified Centor criteria or McIsaac score.5,8 Research findings support Centor and McIsaac scores as useful and valid tools for diagnosis and treatment of patients with acute pharyngitis.17 Additionally, the CDC and the American College of Physicians-American Society of Internal Medicine promote the use of the Centor score for the management of acute pharyngitis in adults.18 To calculate the Centor score, the patient receives 1 point for each of the following: fever, absence of cough, presence of tonsillar exudates, and swollen, tender anterior cervical nodes for a total score ranging from 0 to 4. The McIsaac score adjusts the Centor score to account for age by adding 1 point to the Centor score for those ages 3 to 14 years and subtracting 1 point for those age 45 years and older.5,8 The NP should test for GAS pharyngitis in patients with a Centor score of 2 or higher.5,8

A Monospot test can be considered for EBV in patients with suspected infectious mononucleosis. If the Monospot test is positive, it is considered diagnostic for EBV infection.18 If the test is negative in a patient with a strong clinical suspicion for EBV infection, a definitive diagnosis can be attained with EBV-specific serologic testing using the same sample that yielded the negative Monospot test.18 Alternatively, the Monospot test can be repeated on a serum specimen obtained 7 to 10 days later.18 Patients with high-risk sexual behaviors who present with acute pharyngitis—particularly when accompanied with fever, oral ulcerations, myalgia, or rash—should be tested for acute HSV and/or gonococcal pharyngitis.10


Treatment for viral pharyngitis is supportive, with symptoms generally subsiding over 5 to 6 days on average. While acute viral pharyngitis is non-life threatening, it has negative impacts on a patient's quality of life. Pain from pharyngitis can result in poor nutritional intake, decreased sleep, and shortness of breath.19 The use of oral analgesics, gargling, drinking fluids, and sucking on throat lozenges or popsicles can provide relief of a sore throat.8 Antipyretics can be useful in reducing fever.5,8

Therapeutic options for GAS are aimed at eradication of the pathogen.19 NPs should treat patients with antibiotics only if they have confirmed GAS. Unfortunately, up to 75% of adults with pharyngitis are prescribed antibiotics, even though GAS is only associated with adult pharyngitis in 5% to 15% of cases.6 This inappropriate use of antibiotics certainly raises concerns about antibiotic resistance and rising costs associated with pharyngitis treatment.6 Patients should be treated with an appropriate antibiotic at an appropriate dose for the recommended duration that is likely to eliminate the organism.5,18

- ICD codes: Pharyngitis21
ICD-10-CM code Specificity
Codes for acute upper respiratory infections are built upon the base codes of J00-J06 Appropriate disease specificity coding below
J02 Acute Pharyngitis
  • J02.0 Streptococcal pharyngitis

  • J02.8 Acute pharyngitis due to other specified organisms

  • J02.9 Acute pharyngitis, unspecified

Supplementary codes to identify infectious agent (add to the J02.8 code)
B95 Streptococcus, Staphylococcus, and Enterococcus as the cause of diseases classified elsewhere
  • B95.0 Streptococcus, group A

  • B95.1 Streptococcus, group B

  • B95.2 Enterococcus

  • B95.3 Streptococcus pneumoniae

  • B95.4 Other streptococcus

  • B95.5 Unspecified streptococcus

  • B95.61 Methicillin-susceptible Staphylococcus aureus

  • B95.62 Methicillin-resistant S. aureus

  • B95.7 Other staphylococcus

  • B95.8 Unspecified staphylococcus

B96 Other bacterial agents as the cause of diseases classified elsewhere
B97 Viral agents as the cause of diseases classified elsewhere
  • B97.0 Adenovirus

  • B97.2 Coronavirus

J31.2 Chronic pharyngitis
A54.5 Gonococcal pharyngitis
B00.2 Herpesviral gingivostomatitis and pharyngotonsillitis
  1. J01.0ˆ-J01.4ˆ Acute sinusitis

  2. J01.8 Other acute sinusitis

  3. J01.9 Acute sinusitis, unspecified

  1. ˆAdditional characters required to specify location and whether unspecified or recurren

    • J01.80 Other acute sinusitis

    • J01.81 Other acute recurrent sinusitis

    • J01.90 Acute sinusitis

    • J01.91 Acute recurrent sinusitis, unspecified

  1. J03.0 Streptococcal tonsillitis

  2. J03.8 Acute tonsillitis due to other specified organisms

  3. J03.9 Acute tonsillitis, unspecified

  • J03.00 Acute streptococcal tonsillitis, unspecified

  • J03.01 Acute recurrent streptococcal tonsillitis

  • J03.80 Acute tonsillitis due to other specified organisms

  • J03.81 Acute recurrent tonsillitis due to other specified organisms

  • J03.90 Acute tonsillitis, unspecified

  • J03.91 Acute recurrent tonsillitis, unspecified

  1. J06.0 Acute laryngopharyngitis

  2. J06.9 Acute upper respiratory infection, unspecified

  • J36 Peritonsillar abscess

  • J39.0 Retropharyngeal and parapharyngeal abscess

  • J39.1 Other abscess of pharynx

  • J09.X2 Influenza due to identified novel influenza A virus with other respiratory manifestations

  • J10.1 Influenza due to other identified influenza virus with other respiratory manifestations

  • J11.1 Influenza due to unidentified influenza virus with other respiratory manifestations

Note: List is not comprehensive of all codes within these categories.
Additional character(s) required for further specificity

Penicillin or amoxicillin are the drugs of choice due to the narrow spectrum of activity, infrequency of adverse reactions, and modest cost.5 Both penicillin and amoxicillin are dosed for a 10-day period. For patients with penicillin allergies, first-generation cephalosporins can be used (except in patients with immediate hypersensitivity, such as anaphylaxis, to penicillin) for 10 days, clindamycin or clarithromycin for 10 days, or azithromycin for 5 days.5,16 Patients with recurrent pharyngitis that have diagnostic evidence of GAS can be chronic carriers who have repeated viral infections; in this instance, antibiotics are not recommended.16 A referral to a specialist such as an otolaryngologist is warranted for recurrent infections that do not improve after antibiotic treatment.20

Patients who test positive for STI pharyngitis should be referred for counseling regarding the behavioral, psychosocial, and medical implications of infection.21 All patients with a first episode of HSV should receive antiviral therapy. Recommended regimens include acyclovir, valacyclovir, or famciclovir.21 Treatment of uncomplicated gonococcal pharyngitis is ceftriaxone I.M.22 The NP should schedule patients treated for gonococcal pharyngitis for a test-of-cure 7 to 14 days after treatment.22


The International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) is a morbidity classification published by a joint effort between the CMS and the National Center for Health Statistics.23 The ICD-10-CM is the standard billing code system that is used to submit diagnosis codes for insurance reimbursement. The code with the highest specificity will increase reimbursement. Coding specificity includes reporting all diagnosis codes that identify a person's condition.23

The coding for acute pharyngitis is straightforward as long as acute (J02) is differentiated from chronic pharyngitis (J31.2). It is vital to document the causative agent, if known. For example, J02.0 should be used to indicate acute pharyngitis due to streptococcus. If the cause is due to some other specified organism, then the J02.8 code should be used. The B95-B97 categories of codes should be used with J02.8 to identify the specific causative organism. For example, acute pharyngitis caused by adenovirus would be coded using J02.8 and B97.0. It is important to note that there are certain infectious causes of pharyngitis that are not coded under J02 but are coded relative to the category of the major causative agent. For example, acute pharyngitis caused by herpes is coded B00.2; whereas acute pharyngitis due to gonorrhea is coded A54.5. If the cause of the acute pharyngitis is truly unknown at the time of care, the code J02.9 may be used (see ICD codes: Pharyngitis).

Implications for practice

The role of the NP in managing acute pharyngitis is multifaceted. It is important for the NP to educate patients on preventive strategies to reduce the risk of contracting or transmitting infections by washing their hands, covering their mouth and nose when sneezing or coughing, avoiding contact with others that are ill, and practicing safe sex, as well as about appropriate antibiotic use. Although the majority of cases of acute pharyngitis in adults are viral, 60% to 75% of patients managed in outpatient clinics received antibiotics for a sore throat.4,6,8 An astute NP will manage patients with acute pharyngitis by evaluating airway, breathing, and circulation; considering the patient's history and PE to differentiate between viral, bacterial, and sexually transmitted etiologies; calculating a modified Centor score; considering the benefit of a RADT; and applying treatments accordingly.4 It is important for the NP to follow the recommendations set forth in the guidelines and make appropriate referrals and follow-ups as necessary.


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16. Randel AInfectious Disease Society of America. IDSA updates guideline for managing group A streptococcal pharyngitis. Am Fam Physician. 2013;88(5):338–340.
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18. Miller JM, Binnicker MJ, Campbell S, et al. A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2018 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. 2018;67(6):e1–e94.
19. Catic T, Kapo B, Pintol Z, et al. An instrument for rating quality of life related to sore throat in patients suffering from acute pharyngitis or tonsillitis. Mater Sociomed. 2018;30(1):43–48.
20. Kundu S, Dutta M, Adhikary BK, Ghosh B. Encountering chronic sore throat: how challenging is it for the otolaryngologists. Indian J Otolaryngol Head Neck Surg. 2019;71(suppl 1):176–181.
21. Workowski KA, Bolan GACenters for Disease Control and Prevention. Sexually transmitted diseases treatment guidelines, 2015. MMWR Recomm Rep. 2015;64(RR-03):1–140.
22. St. Cyr S, Barbee L, Workowski KA, et al. Update to CDC's treatment guidelines for gonococcal infection, 2020. MMWR Morb Mortal Wkly Rep. 2020;69(50):1911–1916.
23. ICD-10-CM Official Guidelines for Coding and Reporting. 2019.

acute pharyngitis; bacterial pharyngitis; billing; clinical manifestations; NP; pathophysiology; pharyngitis; primary care; sore throat; treatment; upper respiratory infection; viral pharyngitis

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