Oregon Health Authority Compendium of Acute Respiratory Diseases 07/02/2020

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

I. Agents typified by fever ≥100°F with cough and systemic symptoms (chills, headache, myalgia, malaise, anorexia) Incubation Communicable Mode of Agent Symptoms Reservoir Period Period Transmission Case Definition and Lab-related Information Positive rapid test (sensitivity 50-70%), RT-PCR or isolation of virus on culture (rarely performed at clinical labs). ***************************************** Influenza C not tested at the OSPHL. Fever, cough, Humans, For Influenza A and B: coryza, but spread 3–7 days Mostly droplet; Preferred: nasopharyngeal swab using Dacron polyester myalgia, of novel Possible maybe via or flocked swabs on a plastic shaft, collected 3-7 days Influenza 2 days prostration viruses shedding one day aerosol or after illness onset. Submit swabs in viral transport media. (A, B, C) (1–4 days) from birds before symptom contaminated Store and transport specimens at refrigerated Vomiting, & various onset surfaces temperatures for receipt at the OSPHL within 3 days of diarrhea in mammals specimen collection children is possible

Acceptable: nasal swabs, throat swabs, combination nasopharyngeal swabs (2 swabs in one vial), nasal aspirates, nasal washes, bronchoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, or cell culture isolates.

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 1 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

I. Agents typified by fever ≥100°F with cough and systemic symptoms (chills, headache, myalgia, malaise, anorexia) (continued) Incubation Communicable Mode of Agent Symptoms Reservoir Case Definition and Lab-related Information Period Period Transmission PCR testing for adenovirus and specifically for Adenovirus Depending on adenovirus serotype 14 are available. serotype, can ***************************************** (several present as Preferred: use Dacron polyester or flocked swabs on serotypes. sore throat, a plastic shaft, collected 3-7 days after illness onset. Adeno 7 and 14 “croup” with circulate in runny nose in "Shortly" before Submit swabs in viral transport media. Store and Respiratory Oregon and kids; serotype onset & for transport specimens at refrigerated temperatures for 2–14 days droplets, can Humans have caused 14 commonly duration of receipt at the OSPHL within 3 days of specimen be fecal/oral several causes fever, symptoms collection outbreaks. cough, Acceptable: nasal swabs, throat swabs, combination Adeno 7 is headache, nasopharyngeal swabs (2 swabs in one vial), nasal associated with muscle aches; aspirates, nasal washes, bronchoalveolar lavages, severe occurs any bronchial washes, tracheal aspirates, sputum, lung infections.) time of year. tissue, or cell culture isolates As long as organism is Culture of H. flu from a normally sterile site. Abrupt onset present in ***************************************** fever, discharges from Original testing laboratory will send specimen to the anorexia, nose or throat. OSPHL. OSPHL accepts actively growing isolated Unknown vomiting, Exposure >7 organism in pure culture, on an agar slant, or plate Haemophilus (probably cough, days before Droplet Humans media. Primary specimens from sterile sites are influenzae 2–4 days) lethargy. symptom onset in accepted if previously tested using culture- Headache, case imparts low independent diagnostic tests and approved for stupor suggest risk. Hib cases forwarding to the OSPHL. Store and transport at meningitis. most infectious ambient or refrigerated temperatures for receipt at during the 3 days the OSPHL within 24 hours of culture. prior to sx onset.

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 2 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

Productive Humans Isolation on culture from sputum, though this can be cough, (carriage is difficult. Characteristic gram-positive diplococci on gram fever/chills, As long as the more stain of sputum is suggestive. Streptococcus Unknown shortness of organism common in pneumoniae (probably breath, chest appears in Droplet children ***************************************** (Pneumococcus) 1–4 days) pain. People respiratory than in The OSPHL does not provide this testing. If submitted to look sick! secretions. adults) the OSPHL, will be forwarded for public health Often follows surveillance. Specimen will be obtained in hospital and viral infection. tested in a private laboratory.

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 3 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

productive Some private laboratories also offer testing. cough. Pontiac

fever is accompanied by cough but does not progress to pneumonia or death. Coronavirus 4–5 days Can range from Unknown. Camels; Positive PCR on lower respiratory specimen, serum, or Middle Eastern (2–14 asymptomatic Unknown CDC appears nasopharyngeal or oropharyngeal swab. Respiratory days) to fever, cough, recommends trans- ***************************************** Syndrome and chills, to standard, missible, The OSPHL provides PCR testing for MERS; (MERS) severe contact, and with low Information about specimen collection and handling is respiratory airborne infectivity, available at: (Call ACDP, distress. See: precautions from person www.cdc.gov/coronavirus/mers/guidelines-clinical- pronto, if www.cdc.gov/c to person specimens.html suspected) oronavirus/mer s/interim- guidance.html for testing criteria Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 4 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

Fever, cough, rapidly progressing Coronavirus shortness of Severe Acute breath. CXR Respiratory Viral culture or PCR. Visualization of characteristic virus consistent with Humans, Syndrome Poorly defined; on electron microscopy. Detection of viral antigens on pneumonia or Droplet, Civets (not (SARS) 2–10 days may be up to 21 immunohistochemistry. acute contact many days. respiratory around!) ***************************************** (Call ACDP, distress Not tested by the OSPHL. immediately, if syndrome. Can suspected) also present with milder disease.

Fever, cough, anosmia, ageusia, rapidly progressing Positive nucleic acid amplification test (NAAT) or shortness of breath. CXR antigen test from any respiratory tract specimen. Humans, Coronavirus 4–7 days consistent with 2 days before to Droplet, probably ***************************************** Disease-2019 (2–14 pneumonia or 10 days after contact originally OSPHL offers two different tests for SARS-CoV-2, (COVID-19) days) acute illness onset. from bats the virus that causes COVID-19. For complete respiratory instructions for specimen collection, storage, and distress transport, visit www.healthoregon.org/labtests. syndrome. Can also present with milder disease.

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 5 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

II. Agents associated with severe disease in infants & children Incubation Communicable Mode of Agent Symptoms Reservoir Case Definition and Lab-related Information Period Period Transmission See Pertussis investigative guideline. ***************************************** Collect as soon as possible after illness onset, and not later than 3 weeks or after antibiotics have been Highly started. Bordetella contagious Respiratory For PCR, collect nasopharyngeal specimen using Paroxysmal pertussis during 1st week droplets or coughing w/ Dacron tip swab on a flexible wire shaft and submit 7–10 days of symptoms; direct contact Humans whoop & in a dry plastic specimen tube. Store and transport whooping cough negligible after 5 w/ respiratory vomiting at refrigerated temperatures for receipt at the pertussis days of secretions OSPHL within 24 hours of specimen collection. treatment. For Culture, collect nasopharyngeal specimen using a Dacron tip swab on a flexible wire shaft and submit in Regan-Lowe transport media. Store and transport at refrigerated temperatures for receipt at the OSPHL within 3 days of specimen collection. In infants, RT-PCR, rapid antigen test, viral isolation croup w/ *****************************************Preferred: use barking cough, Dacron polyester or flocked swabs on a plastic shaft, wheezing, 1-5 days after collected 3-7 days after illness onset. Submit swabs in inspiratory onset; longer viral transport media. Store and transport specimens at Respiratory Often 2 Humans, stridor; (weeks) in Droplet, refrigerated temperatures for receipt at the OSPHL syncytial virus days rarely Older infants & the Contact within 3 days of specimen collection. (RSV) (1-8 days) chimpanzees kids/adults immune- Acceptable: nasal swabs, throat swabs, combination have URI, compromised nasopharyngeal swabs (2 swabs in one vial), nasal cough; aspirates, nasal washes, bronchoalveolar lavages, “season” is bronchial washes, tracheal aspirates, sputum, lung Oct.-May tissue, or cell culture isolates

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 6 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

III. Agents associated with exposure to animals or animal settings (kennels, aviaries, abattoirs, laboratories, etc.) Incubation Communicable Mode of Agent Symptoms Reservoir Period Period Transmission Case Definition and Lab-related Information

• Culture and identification from clinical specimens by Laboratory Response Network (LRN)5,6; • Demonstration of B. anthracis antigens in tissues by immunohistochemical staining using both Fever, B. anthracis cell wall and capsule monoclonal malaise, mild antibodies; cough, • Evidence of a four-fold rise in antibodies to shortness of Bacillus breath, Herbivores protective antigen between acute and convalescent anthracis headache, (cattle, goats, sera or a fourfold change in antibodies to protective chills; then Inhaling sheep, bison, antigen in paired convalescent sera using Centers inhalational 1–7 days abrupt onset aerosols from etc.) for Disease Control and Prevention (CDC) Not anthrax (1–60 of sweats, tissues, hair, quantitative anti-PA immunoglobulin G (IgG) ELISA communicable days) spiking fever, wool, hides of Potential testing in an unvaccinated person; (Call ACDP, ARDS & ill herbivores bio- ***************************************** pronto, if shock; terrorism Specimen will be submitted by the original testing suspected) mediastinal agent widening, laboratory. Submit actively growing isolated pleural organism, in pure culture, on an agar slant or plate effusions on media. Store and transport at ambient temperatures CXR for receipt at the OSPHL as soon as possible. Do not freeze. Notify the OSPHL before shipment.

If PCR testing is indicated, please contact the OSPHL to discuss specimen submission requirements.

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 7 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 8 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

III. Agents associated with exposure to animals or animal settings (kennels, aviaries, abattoirs, laboratories, etc.) (continued) Incubation Communicable Mode of Agent Symptoms Reservoir Period Period Transmission Case Definition and Lab-related Information 10 days Acute onset Minimal risk. Inhalation of Psittacine Chlamydia 4-fold rise in psittacosis complement-fixing antibody psittaci (5–14 d) fever, chills, Theoretically desiccated birds titer (to ≥ 1:32) in specimens obtained > 2 weeks headache, possible during bird feces, (parrots, psittacosis kerato- paroxysmal feathers, dust parakeets, apart. PCR can be used in the acute stage of the conjunctivitis, coughing love birds), disease in sputum, pleural fluid and blood. myalgia, rash, pigeons and ***************************************** pneumonia some poultry Birds in the household should be tested by PCR. w/o cough. (primarily (See your vet.) CXR with turkeys & lobar ducks; not consolidation, much in patchy chickens) infiltrates Francisella 3–5 days Rapid onset Not Inhaling Lagomorphs Confirmed: Isolation by culture of F. tularensis in a tularensis (1 – 21 d) high fever, communicable infectious (rabbits, clinical specimen, or a fourfold or greater rise in chills, fatigue, aerosols and hares, etc.), tularemia pleuretic chest contaminated rodents, hard serum antibody titer to F. tularensis antigen between pain, dyspnea, dust ticks, biting acute and convalescent titers. (Call ACDP, lymphadenopa generated flies Presumptive: elevated titers to F. tularensis without pronto, if thy, myalgia, while handling documented fourfold change, in the absence of prior suspected) headache, hides, Potential tularemia vaccination, or detection of F. tularensis in malaise, mild carcasses, bio- a clinical specimen by fluorescent assay. cough; then contaminated terrorism pneumonia, grain; animal agent ***************************************** ARDS or insect bite. For isolation and ID, submit actively growing isolate, in pure culture, on an agar slant or plate media to OSPHL. Store and transport at ambient temps. for receipt at the lab ASAP; notify lab prior to shipment. For antibody testing, submit to the OSPHL according to CDC instructions, see https://www.cdc.gov/laboratory/specimen- submission/detail.html?CDCTestCode=CDC-10314

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 9 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

III. Agents associated with exposure to animals or animal settings (kennels, aviaries, abattoirs, laboratories, etc.) (continued) Incubation Communicable Mode of Agent Symptoms Reservoir Period Period Transmission Case Definition and Lab-related Information Fever, myalgia, GI pain; then abrupt onset Four-fold rise in hantavirus EIA (reactive or not) test ARDS, sepsis IgM and IgG; draw one sample acutely and, if thrombocytop negative, a specimen no sooner than 15 days from Hantavirus enia symptom onset & convalescent 2 weeks after acute No person-to- Inhaling leukocytes, specimen hantavirus 1–7 weeks person aerosolized Rodents hemo- pulmonary transmission rodent excreta ***************************************** concentration; syndrome documented interstitial Submit 5-7 mL blood or 1-2 mL serum or plasma in lymphocyte a red top or serum separator tube. Store and infiltrates, transport at refrigerated temperatures for receipt at alveolar the OSPHL within 5 days. pulmonary edema Rodents, racoons, Sudden onset livestock, fever, dogs, Indirect hemagglutination (titer) Leptospira headache, amphibians, 7 to 12 spp. chills, myalgia Contact with reptiles, ***************************************** days, with Rare person-to- in legs & mucous sealions; a range of person For antibody testing, submit to the OSPHL Leptospirosis conjunctival membranes or animal 2 to 29 transmission according to CDC instructions, available at: Weil's disease suffusion; then ingestion products of days https://www.cdc.gov/laboratory/specimen- (icteric) pneumonia, conception or submission/detail.html?CDCTestCode=CDC-10201 hemoptysis, urine; ARDS contaminated water, soil, mud

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 10 | Page OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

III. Agents associated with exposure to animals or animal settings (kennels, aviaries, abattoirs, laboratories, etc.) (continued) Incubation Communicable Mode of Agent Symptoms Reservoir Case Definition and Lab-related Information Period Period Transmission Isolation by culture from a sputum specimen; four-fold rise in serum antibody titer to Y. pestis F1 antigen in Acute-onset of acute & convalescent serum specimens; antibody titer of fever, chills, ≥1:128 to Y. pestis F1 antigen not explained by past Fleas, wild headache, infection or vaccination; detection of F1 antigen in a From onset of Person-to- rodents (rats, Yersinia pestis malaise & clinical specimen by fluorescent assay symptoms, person squirrels, pneumonic myalgias; then usually w/in transmission prairie dogs), ***************************************** plague cough w/ 2–4 days 24–48hrs of via respiratory pets with For isolation and identification, specimen will be (Call ACDP at bloody (1–7 d) exposure, until droplets fleas submitted by the original testing laboratory. Submit 971-673-1111, sputum, done w/ 72hrs of actively growing isolated organism, in pure culture, on pronto, if pneumonia, appropriate aerosol Potential an agar slant or plate media. Store and transport at suspected) ARDS, antibiotics (bioterrorism) bioterrorism ambient temperatures for receipt at the OSPHL as soon circulatory agent as possible. Notify the OSPHL before shipment. collapse & For antibody testing, submit to the OSPHL according to death CDC instructions, available at: https://www.cdc.gov/laboratory/specimen- submission/detail.html?CDCTestCode=CDC-10419

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 11 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

IV. Other pathogens Incubation Communicable Mode of Agent Symptoms Reservoir Case Definition and Lab-related Information Period Period Transmission Classically Humans, cough, See TB See TB mammals Myco- blood in Guidelines: Guidelines: (elephant bacterium sputum, Aerosol See TB Guidelines: healthoregon.org/iguides s, cattle, tuberculosis fever, some night primates) sweats. URI possible with Isolation on culture is not that easy. PCR may be cough/congest helpful, as is a fourfold rise in complement fixation ion. Sub-acute Unclear. antibody titers on samples collected 4 weeks apart. Mycoplasma “Walking Perhaps ten or 1-4 weeks Droplet Humans ***************************************** pneumonia” more days after pneumoniae PCR and culture can be done on sputum, in ~10% w onset. oropharyngeal swabs, or nasopharyngeal swabs. usually non- productive Testing for Mycoplasma is available through cough/fever. commercial labs, but not through OSPHL. Isolation on culture Types 1 and 2 ***************************************** commonly The OSPHL cannot test for parainfluenza virus type cause URIs, 4. For parainfluenza types 1-3: or croup in Preferred: using Dacron polyester or flocked swabs kids (barking Often 1 day before to on a plastic shaft, collected 3-7 days after illness Parainfluenza cough or Droplet, ~2 days 5 days after sx Humans onset. Submit swabs in viral transport media. Store virus types 1-4 hoarseness); Contact (0.5-7 d) onset. and transport at refrigerated temperatures for receipt Type 3 can at the OSPHL within 3 days. lead to bronchiolitis Acceptable: nasal or throat swabs, combined and nasopharyngeal swabs (2 swabs in one vial), nasal pneumonia. aspirates or washes, bronchoalveolar lavages, bronchial washes, tracheal aspirates, sputum, lung tissue, or cell culture isolates.

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 12 | Page

OREGON HEALTH AUTHORITY COMPENDIUM OF ACUTE RESPIRATORY DISEASES 07/02/2020

Revision History June 2020 – Added COVID-19 and adjusted formatting (Cieslak, Leman, Byster) April 2018 – Pathogen descriptions, lab confirmation instructions, OSPHL address and formatting updated; added MERS and removed Q Fever (Allain, Ariail, Boyd, Crawford, DeBess, Humphrey, Leman, Liko, Poissant, Scott, Tran) April 2012 – Contact information for OSPHL and availability of testing at OSPHL updated. October 2010 – Original posted

Oregon State Public Health Lab (OSPHL): 7202 NE Evergreen Parkway, Suite 100, Hillsboro, OR 97214/ 503.693.4100

Acute and Communicable Disease Prevention (ACDP) 800 NE Oregon St. Suite 772, Portland, Oregon 97232 / 971-673-1111 13 | Page