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B73 COVID-19

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Procedural Guidance for DPH Staff

COVID-19 – Core Information

  • Agent, Identification, Differential Diagnosis and Diagnosis sections
  • Incubation, Reservoirs, Source, and Transmission sections
  • Communicability/Period of Infectiousness section
  • Determining Close Contacts section
  • Specific Treatment and Immunity section
  • Diagnostic Procedures section
  • Vaccinated Persons section
  • Patients with a History of Recent Recovery from COVID-19 section

B73 COVID Chapters

  • COVID-19 Community Care Facilities webpage
  • Adult Day Care Centers webpage
  • People Experiencing Homelessness (PEH) webpage
  • Early Care and Education and K-12 Schools webpage
  • Institutes of Higher Education webpage
  • Correctional and Detention Facilities webpage
  • Non-Residential Settings webpage
  • Skilled Nursing Facilities webpage


A human coronavirus (SARS-CoV-2) first identified in December 2019 causes COVID-19.


  1. Symptoms:
    Patients with SARS-C0V-2 infection can experience a range of clinical manifestations, from no symptoms to critical illness. Patients who are older or who have underlying medical conditions are at higher risk of progressing to severe COVID-19, especially if they are unvaccinated or under vaccinated.

    Symptoms commonly reported among adults with COVID-19 include:

    • Fever
    • Cough
    • Shortness of breath or difficulty breathing
    • New loss of taste or smell
    • Chills/rigors
    • Myalgias
    • Congestion or runny nose
    • Nausea or vomiting
    • Diarrhea
    • Sore throat
    • Fatigue
    • Headache

    Signs and symptoms of COVID-19 in children vary by age of the child and are usually milder compared to adults.

    See NIH Clinical Spectrum of SARS-CoV-2 Infection for a more detailed discussion of COVID-19 clinical signs and symptoms including severity of illness categories.

  2. Differential Diagnosis: Other agents that cause febrile respiratory illnesses including, but not limited to, influenza viruses, respiratory syncytial virus, parainfluenza viruses, Streptococcus pneumoniae, Legionella species, mycoplasma, and other atypical pneumonia agents.

  3. Diagnosis:
    CSTE (to be used in outbreak settings and for close contacts)

Case Classification


  • Meets supportive laboratory evidence†† with no prior history of being a confirmed or probable case.

†† For suspect cases, jurisdictions may opt to place them in a registry for other epidemiological analyses or investigate to determine probable or confirmed status.


  • Meets clinical criteria AND epidemiologic linkage with no confirmatory or presumptive laboratory evidence for SARS-CoV-2, OR
  • Meets presumptive laboratory evidence, OR
  • Meets vital records criteria with no confirmatory laboratory evidence for SARS-CoV-2.


  • Meets confirmatory laboratory evidence.

Clinical Criteria

In the absence of a more likely diagnosis:

  • Acute onset or worsening if at least two of the following symptoms or signs:
    • fever (measured or subjective),
    • chills,
    • rigors,
    • myalgia,
    • headache,
    • sore throat,
    • nausea or vomiting,
    • diarrhea,
    • fatigue,
    • congestion or runny nose.


  • Acute onset or worsening of any one of the following symptoms or signs:
    • cough,
    • shortness of breath,
    • difficulty breathing,
    • olfactory disorder,
    • taste disorder,
    • confusion or change in mental status,
    • persistent pain or pressure in the chest,
    • pale, gray, or blue colored skin, lips, or nail beds, depending on skin tone,
    • inability to wake or stay awake.


  • Severe respiratory illness with at least one of the following:
    • Clinical or radiographic evidence of pneumonia,
    • Acute respiratory distress syndrome (ARDS).

Laboratory Criteria

Confirmed laboratory evidence:

  • Detection of SARS-CoV-2 ribonucleic acid (RNA) in a post-mortem respiratory swab OR clinical specimen using a diagnostic molecular amplification test performed by a Clinical Laboratory Improvement Amendments (CLIA)-certified provider, OR
  • Detection of SARS-CoV-2 by genomic sequencing.

Presumptive laboratory evidence:

  • Detection of SARS-CoV-2 specific antigen in a post mortem obtained respiratory swab OR clinical specimen using a diagnostic test performed by a CLIA-certified provider.

Supportive laboratory evidence:

  • Detection of antibody in serum, plasma, or whole blood specific to natural infection with SARS-CoV-2 (antibody to nucleocapsid protein), OR
  • Detection of SARS-CoV-2 specific antigen by immunocytochemistry in an autopsy specimen, OR
  • Detection of SARS-CoV-2 RNA or specific antigen using a test performed without CLIA oversight.


Omicron has a short incubation period. Estimated to be 2-4 days.




Nasal and pharyngeal secretions.


Omicron is very infectious. More transmissible than original SARS-CoV-2 and Delta variant. Anyone with Omicron infection, regardless of vaccination status or whether or not they have symptoms, can spread the virus to others. Data suggest that Omicron can cause reinfection, even in people who have recovered from COVID-19. See CDC Variants of the Virus.

There are three principal ways in which infectious exposures to respiratory fluids carrying SARS-CoV-2 occur:

  1. Inhalation of aerosol particles and small droplets. The concentration of these small droplets is generally highest within three to six feet of an infected person. However, these small particles can remain airborne, posing a risk at a greater distance in enclosed spaces.
  2. Deposition of virus in larger exhaled droplets and particles onto mucous membranes. Risk of transmission is highest close to an infected person and decreases with distance.
  3. Touching mucous membranes with hands contaminated by exhaled respiratory fluids or by fomites. Note: Fomite transmission likely does not cause a substantial percentage of infections.

Inhalation plays a larger role than previously believed, as aerosolized particles can remain in the air for minutes to hours. This is more likely in enclosed spaces with poor ventilation, especially if an infectious person spends an extended period in that space or if they are participating in activities that increase exhalation of respiratory fluids, such as vigorous exercise, singing, or shouting.

Read CDC's Scientific Brief: SARS-CoV-2 Transmission.

For CDC patient-friendly information, see How COVID-19 Spreads.

Communicability/Period of Infectiousness

CDC has been monitoring the emerging science on when and for how long a person is maximally infectious with Omicron. Per the CDC, the majority of SARS-CoV-2 transmission occurs in the 1-2 days prior to onset of symptoms and the 2-3 days after.

A person with COVID-19 is considered to be infectious beginning 2 days before their symptoms began until their isolation period ends. If they test positive for COVID-19 but remain asymptomatic, they are considered to be infectious from 2 days before the test was collected until their isolation ends.

When isolation can end:

Everyone with COVID-19 must isolate for at least 5 days.

  • Isolation can end after Day 5 (i.e., on Day 6 - Day 10) ONLY if all of the following criteria are met:
  1. A COVID-19 viral test collected on Day 5 or later is negative
  2. No fever for at least 24 hours without the use of fever reducing medicine
  3. Other symptoms are not present or are improving


  • Isolation can end after Day 10 (i.e., on Day 11)* if:
  1. No fever for at least 24 hours without the use of fever reducing medicine

For the general public, see Isolation Instructions for People with COVID-19.

* The CDC recommends extending isolation for patients who were severely ill or who are moderately to severely immunocompromised.

For patients with severe to critical COVID-19 illness (e.g., required hospitalization, intensive care, or ventilation support) who are not immunocompromised, the CDC recommends extending the duration of isolation and precautions from 10 days to up to 20 days from illness onset. This is because they may produce replication-competent virus beyond 10 days.

For patients who are moderately to severely immunocompromised (regardless of symptoms or COVID-19 illness severity) the CDC recommends an isolation period of at least 20 days, ending isolation in conjunction with a test-based strategy and consultation with an infectious disease specialist and infection control experts. to determine the appropriate duration of isolation and precautions. This is because moderately or severely immunocompromised patients may produce replication-competent virus beyond 20 days.

Determining Close Contacts

A close contact is a person with exposure to a laboratory-confirmed or clinical case of COVID-19 during the period of infectiousness of the case (see Communicability/Period of Infectiousness above). This is from 2 days before symptom onset (or date of first positive lab test for asymptomatic persons) until the case meets criteria for discontinuing isolation/transmission-based precautions.

Effective October 14, 2022, by order of the State Public Health Officer, who is considered a close contact varies based on the size of the shared indoor space:

  • In indoor 400,000 or fewer cubic feet per floor (e.g., home, clinic waiting room, airplane, etc.), a close contact is defined as anyone sharing the same indoor airspace for a cumulative total of 15 minutes or more over a 24-hour period while the case was infectious
  • In large indoor spaces greater than 400,000 cubic feet per floor (such as open-floor-plan offices, warehouses, large retail stores, manufacturing, or food processing facilities), a close contact is defined as someone being within 6 feet for a cumulative total of 15 minutes or more over a 24-hour period while the case was infectious.
  • Spaces that are separated by floor-to-ceiling walls (e.g., offices, suites, rooms, waiting areas, bathrooms, or break or eating areas that are separated by floor-to-ceiling walls) must be considered distinct indoor airspaces.

For additional details see CDPH Order Q&A.

People are considered close contacts regardless of the use of face masks by the case or contact. Exception: Cal/OSHA states that employees are not a close contact if they wore a respirator required by the employer and used in compliance with section 5144, whenever they were sharing the same airspace of the COVID-19 case while they were infectious.

See site specific B73 for more specific guidance on determining close contacts in different settings.

For general public, see Instructions for Close Contacts at ph.lacounty.gov/covidcontacts.

Specific Treatment

See the NIH COVID-19 Treatment Guidelines for comprehensive information on the medical management of COVID-19 prepared by the COVID-19 Treatment Guidelines Panel. Providers should make treatment decisions based on currently available evidence.

Key points regarding outpatient therapeutics:

  • Outpatient antiviral therapeutics are widely available but underused. This is especially true in communities of color, low-income communities, and in long term care facilities.
  • The majority of adults and some children with symptomatic COVID-19 are eligible for antiviral treatment. This includes people who are not up to date with COVID vaccinations, people in a racial or ethnic minority group, people with disabilities and common underlying health conditions including obesity, depression, smoking (former or present), and physical inactivity. See CDC Risk Factors for Severe COVID-19.
  • Three antiviral therapies are available. Paxlovid, IV remdesivir (Veklury), and molnupiravir (Lagevrio). Paxlovid is the preferred treatment for most adults and children (12 years of age and older weighing at least 40 kg). Many commonly used medications can be safely co-administered with Paxlovid despite potential for drug-drug interaction. Guidance is available on simple steps (such as brief suspension or dose reduction) to avoid significant interactions with commonly prescribed medications.
  • Antiviral treatment of outpatients at risk for severe COVID-19 reduces their risk of hospitalization and death. Recent studies of Paxlovid in highly COVID-19 immune populations demonstrate significant reductions in hospitalizations and deaths among patients 18 and older who had risk factors for severe disease with the largest benefits in unvaccinated patients and in patients who are ≥65 years-old and/or immunocompromised (regardless of vaccination/previous infection).

  • To be eligible for outpatient therapy, patients must meet all of the following:
    1. Have mild or moderate COVID-19 illness
    2. Be within 5 days of symptoms onset for Paxlovid and molnupirivir or 7 days of symptom onset for IV remdesivir
    3. Have one or more risk factors for severe COVID-19 including:
      • Age over 50 years, especially those 65 and older, regardless of the presence of a medical condition
      • Being unvaccinated or not being up to date on COVID-19 vaccinations
      • Being in a racial or ethnic minority group
      • Having common underlying health conditions and behaviors such as physical inactivity, obesity, depression, smoking (former or present), and disabilities. See CDC comprehensive discussion.

See LAC DPH outpatient therapeutics resources:


Natural immunity: Natural immunity from prior SARS-CoV-2 viral variants does not appear to be protective against Omicron subvariants. Among other human coronaviruses, reinfection appears to occur variably over time after onset of infection. The likelihood of re-infection is expected to increase over time because of waning immunity and the possibility of exposure to virus variants. In addition, the level of protection after infection may vary depending on how mild or severe the illness was as well as the person's age.

Vaccine-induced immunity: Currently authorized COVID-19 vaccines remain effective at preventing severe illness, hospitalization, and death against SARS-CoV2 including Omicron.  While efficacy wanes over time, booster doses restore vaccine efficacy for severe outcomes. See CDC COVID-19 Vaccine Effectiveness.

See CDC Science Brief-Immune Response to Infection and Vaccination

Diagnostic Procedures

Clinical and epidemiologic histories are required to aid in diagnosis. Direct viral detection methods with sensitive molecular tests (e.g. RT-PCR) are recommended for diagnosing current infection with SARS-CoV-2. Antigen tests and over the counter (OTC) self-tests can also be used to diagnose acute infection but they are less accurate than PCR tests.

When using lower sensitivity assays (e.g., antigen tests, some molecular tests, OTC self-tests), negative results are considered presumptive and confirmation with RT-PCR is recommended, especially if important for clinical management or infection control.

Serological testing is not a standard part of outbreak investigation.

See CDC Testing for SARS-CoV-2 Infection for an overview of test types.

Facilities are encouraged to test through a commercial lab. Facilities should follow the specimen collection and pick-up instructions as per the facility’s designated commercial clinical laboratory. They should work directly with the clinical laboratory for all questions regarding specimen collection and transport.

See Laboratories Providing Diagnostic Testing for resources to support organizations identify a laboratory provider that best fits their needs.

PHL SARS CoV-2 PCR Specimen Collection

Upper Respiratory Specimen--for initial diagnostic testing, collect at least one upper respiratory specimen.

Any of the following specimens are acceptable:

  • Nasopharyngeal swab
  • Oropharyngeal swab
  • Combined nasopharyngeal/oropharyngeal swab
  • Nasal swab
    • Nasal mid-turbinate swab
    • Anterior nares swab
  • Combined nasal/oropharyngeal swab
  • Nasopharyngeal wash/aspirate
  • Nasal wash/aspirate

Swabs: Acceptable swab types include synthetic fiber swabs (flocked or spun polyester) with plastic or wire shafts. Do not use calcium alginate swabs or cotton swabs with wooden shafts. Place swab in a minimum of 1-3 mL viral transport media, liquid Amies, or saline.

Aspirates and washes: collect 1.5-3.0 mL in a sterile, leak-proof container.

Lower respiratory tract specimens--may be required for patients presenting with severe disease or fatal cases. Acceptable lower respiratory tract specimens include sputum, bronchoalveolar lavage, tracheal aspirate, pleural fluid, lung swab, or lung biopsy. Collect lower respiratory tract specimens in a sterile, leak-proof container. Lung swab should be submitted in viral transport media. A minimum of 2-3 mL is needed for sputum, lavage and aspirates.

Storage: Refrigerate specimens at 2-8°C and transport on cold pack. If specimen storage exceeds 3 days, freeze specimen at ≤ -70°C and ship on dry ice.

For more information see:

  • Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 Guidelines
  • Collection and Submission of Postmortem Specimens from Deceased Persons with Known or Suspected COVID-19 Guidance

Vaccinated Persons

A person is considered up to date with their COVID-19 vaccines when they have received all recommended doses in the primary series AND have received all recommended booster doses, when eligible. See COVID-19 Vaccine Schedules.

See CDC Stay Up to Date with Your COVID-19 Vaccines Including Boosters

Patients with a History of Recent Recovery from COVID-19

A patient with a history of recent recovery from COVID-19 is defined as a person with a positive viral COVID-19 test within the past 3 months (90 days) who has recovered from the previous infection. Recovered means they are no longer considered infectious (i.e., their isolation period has ended).

If the patient had symptoms with their most recent infection, the 90 days are from the onset of the initial COVID-19 symptoms. If they never had symptoms, then the 90 days are from the date of collection of the first positive viral COVID-19 test.

If the recently recovered person

Is asymptomatic

  • If they they have close contact with a COVID-19 case, they are not required to test, quarantine, nor be restricted from work. They must follow the Instructions for Close Contacts including wearing a highly protective mask around others and monitor their health for 10 days.
  • If they have close contact with a COVID-19 case and their first positive test was:
    • <30 days prior -- no viral testing is generally recommended
    • 31-90 days prior -- antigen testing is recommended

Develops new symptoms consistent with COVID-19 illness

  • Testing with antigen tests is recommended, especially if there is no alternative diagnosis and/or the symptoms developed within 10 days after close contact to a case.
  • They should be instructed to self-isolate pending clinical evaluation and the results of SARS-CoV-2 testing, if performed.


Immunocompetent patients who have recovered from acute COVID-19 infection can continue to have detectable SARS-CoV-2 RNA in upper respiratory specimens for 3 months after illness onset and persistent positive antigen tests are possible for at least 24 days. Replication-competent virus has not been reliably recovered from such patients, and they are not likely infectious.

Antigen testing of asymptomatic close contacts is recommended to identify a new infection if 31-90 days have passed since their first positive test. This is because persistent antigen positivity is unlikely after a month and because the probability of SARS-CoV-2 reinfection increases with time due to exposure to viral variants and waning immunity.

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