TABLE OF CONTENTS
- INTRODUCTION COVID-19, INFLUENZA, AND OTHER RESPIRATORY VIRUS TESTING
- COVID-19 AND INFLUENZA DUAL TESTING
- DIAGNOSTIC COVID-19 AND INFLUENZA TESTING FOR SYMPTOMATIC PATIENTS
- TABLE 6.1 RECOMMENDED RESPIRATORY VIRAL TESTING BY CLINICAL PRESENTATION, INCLUDING CONFIRMATORY PCR TESTING
- STRATEGIES TO MAXIMIZE SENSITIVITY OF COVID-19 AND INFLUENZA TESTING
- PATIENT EDUCATION FOR VIRAL TESTING FOR COVID-19 AND INFLUENZA
- TESTING CONSIDERATIONS FOR COVID-19 AND INFLUENZA SINGLE OR DUAL-PATHOGEN OUTBREAKS
- COVID-19 TEST TYPES
- TABLE 6.2 OVERVIEW OF TEST TYPES FOR COVID-19
- TABLE 6.3 COVID-19 TESTING DEFINITIONS AND STRATEGIES
- COVID-19 NUCLEIC ACID AMPLIFICATION (NAAT)/PCR TESTING
- COVID-19 RAPID ANTIGEN TESTING
- COVID-19 SEROLOGY (ANTIBODY) TESTING
- COVID-19 OUTBREAK RESPONSE TESTING
- PRIORITIZING CONTACTS
- COHORTS: COVID-19 MASS TESTING
- COVID-19 EMPLOYEE TESTING DURING OUTBREAKS
- COVID-19 TESTING OF EXPOSED QUARANTINED PATIENTS AND PRIOR TO RELEASE FROM QUARANTINE
- ROUTINE AND SURVEILLANCE COVID-19 TESTING AMONG ASYMPTOMATIC AND NON-EXPOSED PATIENTS
- ROUTINE TESTING OF NON-EXPOSED ASYMPTOMATIC PATIENTS AT HIGHER RISK OF COVID-19 MORBIDITY AND MORTALITY
- ROUTINE COVID-19 TESTING OF INMATE WORKERS
- COVID-19 TESTING OF TRANSFERS
- COVID-19 TESTING OF EXPEDITED RELEASES/PAROLEES
- COVID-19 PUBLIC HEALTH SURVEILLANCE TESTING
- CONCERN FOR COVID-19 FALSE-POSITIVES: WHAT TO DO
- IF YOUR PATIENT IS DEEMED A FALSE POSITIVE
- RE-TESTING PREVIOUSLY POSITIVE PATIENTS AFTER RECOVERY FROM COVID-19
- SUMMARY OF LITERATURE ON COVID-19 VIRAL SHEDDING AND RE-INFECTIONS
- POTENTIAL COVID-19 RE-INFECTIONS
- INFLUENZA VIRAL TESTING
- INFLUENZA TEST TYPES
- INFLUENZA OUTBREAK TESTING
- OTHER RESPIRATORY VIRUS TESTING CONSIDERATIONS
- APPENDIX 5: COVID-19 CASE AND CONTACT SHAREPOINT REPORTING TOOL
- APPENDIX 9: MEMO TEMPLATE FOR NOTIFICATION OF COVID-19 CASES AND CONTACTS RELEASED TO THE COMMUNITY
- APPENDIX 12: SAMPLE LOCAL OPERATING PROCEDURE (LOP) FOR COVID-19 COUNTY TESTING
- APPENDIX 13: COVID SCREENING AND TESTING MATRIX FOR PATIENT MOVEMENT
- APPENDIX 19: COVID-19 AND INFLUENZA SPECIMEN COLLECTION AND TEST ORDERING INFORMATION
- APPENDIX 21: CASE ENTRY FORM FOR RE-INFECTION EVALUATION
1. INTRODUCTION COVID-19, INFLUENZA, AND OTHER RESPIRATORY VIRUS TESTING
This section contains information on diagnostic tests and testing strategies for COVID-19, influenza, and other respiratory pathogens. Influenza specific and other respiratory pathogen guidance are located at the bottom of this section.
It is impossible to reliably distinguish between influenza and COVID-19 clinically (see the Reported Symptoms of COVID-19, Influenza, and Respiratory Syncytial Virus table – Table 5.1). For details on when to test for both influenza and COVID-19, see the subsection Diagnostic COVID-19 and Influenza Testing for Symptomatic Patients.
The onset of the annual influenza season and/or the prevalence of influenza is designated by the California Department of Public Health (CDPH) when prevalence is “Local” or higher (See CDPH Weekly Influenza Surveillance Reports).
Always keep a differential in mind and use clinical judgment on the need for other viral pathogen testing. See the subsections in the Clinical Manifestations section: Differential Diagnosis of Influenza-Like Illness and Clinical Manifestations of Other Respiratory Pathogens.
Until each annual influenza season ends, there will likely be COVID-influenza dual pathogen outbreaks (see the Public Health Definitions section). At each facility, please assess the stock of testing supplies, including collection swabs for COVID-19 and influenza PCR, the COVID-19/influenza combination PCR test, the COVID-19 rapid antigen test, the rapid influenza test (RIDT), and the point of care (POC) COVID-19/influenza combination test.
2. COVID-19 AND INFLUENZA DUAL TESTING
DIAGNOSTIC COVID-19 AND INFLUENZA TESTING FOR SYMPTOMATIC PATIENTS
The symptoms of different respiratory pathogens are very similar. See the Reported Symptoms of COVID-19, Influenza, and Respiratory Syncytial Virus (RSV) table (Table 5.1).
At all times, all patients with ILI symptoms (including those who develop symptoms in quarantine for an index influenza or COVID-19 case) need testing for both COVID-19 and influenza.
Once either the annual influenza season arrives, there are community influenza cases, or an outbreak has occurred (at least one lab-confirmed case of influenza in the setting of a cluster [2 or more cases] of ILI within 72 hours), test all patients with symptoms listed in the Reported Symptoms of COVID-19, Influenza, and RSV table (Table 5.1) for both COVID-19 and influenza. A combination influenza/SARS-CoV-2 POC and PCR test is now available. Please refer to Appendix 19 for more information on the test itself.
Influenza testing should occur regardless of whether the patient was vaccinated or not.
Always use clinical judgment on the need to test for viral pathogens other than COVID-19, including influenza
Please see Table 6.1 for helpful guidance on testing indications for COVID-19 and influenza in different clinical scenarios.
Patients presenting with symptoms of pneumonia (subjective fever or temperature >100° F, cough, or shortness of breath) should be prioritized for testing. Patients with these symptoms who are over age 65 or with medical comorbidities are at risk for complications and are the highest priority for COVID-19 and influenza testing (see Differential Diagnosis subsection in the Clinical Manifestations section). Please refer to the high risk for severe disease tables for COVID-19 (Table 5.3) and influenza (Table 5.5). RSV should also be considered in this vulnerable population and ordered if clinically indicated. The next priority would be those at risk of being exposed or are a high risk of transmitting to others (e.g., an inmate worker with multiple contacts or resides in dorm housing).
Repeat testing is recommended for patients with a high clinical suspicion of COVID-19 or influenza, but an initial negative test.
Testing is not recommended for explained symptoms such as typical allergic symptoms in a patient with a known history or other chronic conditions.
Note: Patients with undiagnosed symptoms or requiring POC confirmation should be housed in single cells with closed solid doors and not with any other cohort.
Symptomatic patients who refuse testing will still need to be isolated in single cells with solid walls and doors and complete the COVID-19 release from isolation criteria when exposed to influenza or COVID-19 or both. Please refer to the Control Strategies for Suspect and Confirmed section for more details on isolation.
Symptomatic patients require testing regardless of whether they are < or >90 days out from their initial COVID-19 infection (from the onset of symptoms or first positive test if asymptomatic). See the discussion below regarding re-positives.
STRATEGIES TO MAXIMIZE SENSITIVITY OF COVID-19 AND INFLUENZA TESTING
- Test early:
- COVID-19: The Centers for Disease Control (CDC) recommend that specimens should be collected as soon as possible once a suspect case is identified, regardless of the time of symptom onset. Testing in the first 5 days of symptoms will give the best sensitivity for both antigen testing and PCR for COVID-19. Viral load is highest in respiratory specimens early on in the disease when symptoms tend to be mild (the first five days). The median time to a negative PCR is 9 days. Studies show a patient with COVID-19 may have a negative upper respiratory PCR sample, while the virus can still be found in the lower respiratory tract in a patient with pneumonia.
- Influenza: Specimens should be collected as soon as possible, preferably within the first 24-72 hours of symptoms onset.
- Use the appropriate collection technique:
Use anterior nares (AN) and oropharyngeal (OP), or nasopharyngeal (NP) and OP collection together, if possible, for either influenza or COVID-19 (see Appendix 19 on this topic).
- Test frequently (COVID-19):
Using a lower sensitivity test like the antigen Sofia 2 test for COVID-19 or influenza more often is an excellent way to increase sensitivity. Repeat testing as much as every 2-3 days can push the sensitivity to approximately 99%. Since the duration of influenza is much shorter than COVID-19, the utility of repeat testing will best be suited for COVID-19.
PATIENT EDUCATION FOR VIRAL TESTING FOR COVID-19 AND INFLUENZA
Part of testing is education. Patients need information regarding why testing is important, symptoms of COVID-19 and influenza, availability of testing, risks of getting infected, and transmission prevention. Patients will need to know why they need testing for influenza even though they received an influenza vaccine. Patients will need to understand that COVID-19 precautions will outweigh influenza when in doubt. If patients receive COVID-19 or influenza testing and have not been vaccinated for influenza, this education is an opportune time to advocate for vaccine importance.
A plan for giving test results and education for COVID-19 and influenza should be in place. See patient education resources on COVID-19 testing, isolation, and recovery. Also, see the nursing scripts on discussing COVID-19 isolation with patients and the influenza patient education resources.
TESTING CONSIDERATIONS FOR COVID-19 AND INFLUENZA SINGLE OR DUAL-PATHOGEN OUTBREAKS
It is important to recognize that outbreaks of respiratory viruses may occur alone or together, making testing and control more complicated. The occurrence of a dual outbreak is likely during any influenza season where COVID-19 viral circulation remains. Early testing, isolation of symptomatic patients, quarantine of contacts, and COVID-19 quarantine testing of contacts is crucial to control an outbreak. Note: persons quarantined for influenza only do not require testing.
Symptom and temperature screening alone is inadequate to promptly identify and isolate infected persons in congregate settings such as correctional and detention facilities. During the influenza season, ILI symptoms could be influenza or a co-infection, or any number of self-limited winter upper respiratory viral pathogens. See the Reported Symptoms of COVID-19, Influenza, and RSV table (Table 5.1). Persons with COVID-19, in particular, can be asymptomatic, or symptoms can be subtle and non-specific. In addition, incarcerated persons may be reluctant to report symptoms, even with active screening. Asymptomatic or pre-symptomatic staff or residents may contribute to transmission. Recent data from COVID-19 outbreaks indicate that symptom-based testing can fail to identify more than 80% of COVID-19 cases in these congregate settings. Influenza has a pre-symptomatic phase of 1 day before symptoms. There are also a high number of asymptomatic influenza cases, but the role in transmission is unclear.
Testing does not replace or preclude other infection prevention and control interventions, including case investigation, isolation of infected individuals, quarantine of exposed individuals, surveillance of quarantined individuals, screening of employees at the start of a shift for signs and symptoms of COVID-19 or influenza, universal use of cloth face coverings by staff and inmates for source control, use of recommended personal protective equipment (PPE) by staff working with suspect and confirmed cases for either illness, and environmental cleaning and disinfection (see Environmental Infection Control).
Order supplies in preparation for dual outbreaks (see Appendix 19 for more information). Please refer to the update on Ordering Sofia-2 Compatible COVID19 Testing Kits (CDCR networking is required for access) and Appendix 19 for more information on laboratory specifications.
3. COVID-19 TEST TYPES
See Appendix 19 for collection and laboratory details, Table 6.2 for a summary of the different test types for COVID-19, Table 6.3 for an overview of the different testing strategies for COVID-19 and their definitions, and Appendix 8 for a summary of the Infectious Diseases Society of America (IDSA) SARS-CoV-2 testing recommendations.
COVID-19 NUCLEIC ACID AMPLIFICATION (NAAT)/PCR TESTING
Quest labs should be considered the first-line COVID-19 testing laboratory. Quest provides a high-quality PCR with a turn-around time of typically 2-3 days and should be used as much as is practical before using a third party, non-electronic health records system (EHRS) interfaced laboratory.
There are SARS-CoV-2 (COVID-19) only Quest PCR tests and now a COVID-19 and influenza combination test. The EHRS order for the combination test is being built and will be available soon.
In the event of prolonged turn-around times with Quest, testing may be available through the local health department (LHD). Each institution should have a local operating procedure (LOP) for accessing COVID-19 testing through the county. When testing outside of Quest is necessary, the LHD will serve as the liaison to access other laboratories, such as the University of California, San Francisco (UCSF) Biohub.
Requesting Quest COVID-19 Test Kits: For information on ordering test kits, see Appendix 19.
COVID-19 RAPID ANTIGEN TESTING
The Quidel Sofia 2 Clinical Laboratory Improvement Amendments (CLIA)-waived rapid antigen test uses an immunofluorescent assay for a COVID-19 antigen. This POC test accurately detects viral proteins in about 15 minutes. COVID-19-influenza combination POC test cassettes are now available. Refer to the COVID-19 Antigen Test Ordering Information and FAQs in Appendix 19 the Quidel Sofia2 SARS + Flu Antigen information website, and the Sofia 2 device information on Quidel’s website (User Manual, Quick Start Guide, and FAQs are under “Product Documentation” near the bottom of the page).
Confirmation of COVID-19 POC (Rapid Antigen) Testing
All positive POC tests need to be confirmed using RT-PCR. See Table 6.1. Patients who are within the first 90 days of being resolved should not be tested unless they develop symptoms. See the section on Re-Testing Previously Positive Patients after Recovery from COVID-19.
Patients who test positive by POC have a presumptive diagnosis of COVID-19 and should be considered infectious. These patients should be isolated in single-person isolation with solid walls and a solid door pending confirmation by PCR. Because of the risk that the POC is a false positive, these patients should not be housed in cohort-isolation with other COVID-19 patients until PCR confirms the diagnosis.
Negative POC tests need to be confirmed using RT-PCR if the patient is symptomatic or there is a clinical suspicion for infection. See Table 6.1.
COVID-19 SEROLOGY (ANTIBODY) TESTING
At this time, serology testing for COVID-19 is not recommended for determining COVID-19 immunity. Antibodies become detectable about 2 weeks after the start of the infection. In addition to concerns with possible cross-reactivity with other coronaviruses, which and what levels of antibodies might confer immunity is unknown, and patients vary widely in their antibody response. According to the CDC, antibody test results should not be used to group people in correctional facilities in actionable cohorts.
Please refer to the Overview of Testing for COVID-19 table (Table 6.2) for more details on indications for COVID-19 viral testing.
4. COVID-19 OUTBREAK RESPONSE TESTING
When a COVID-19 outbreak is suspected based on the identification of one or more PCR-confirmed cases among inmates, institutions should immediately notify and engage the local public health department and the Public Health Branch (PHB) to support integrated staff-inmate contact investigations and consult on creating testing strategies. The PHB is available for consultation: CDCRCCHCSPublicHealthBranch@cdcr.ca.gov.
See Table 6.3, which describes the testing definitions and strategies, including the goals, timing, and frequency of testing.
As soon as possible, after one or more COVID-19 positive individuals (patients or staff) are identified in a facility or housing unit, outbreak response testing should be directed to exposed individuals susceptible to infection. Broad-based testing strategies, including testing of asymptomatic patients in the entire facility or institution, should be used to determine the extent of COVID-19 spread within the facility. Early resolved patients less than 90 days from their primary infection should not be tested unless they develop symptoms.
Testing strategies should consider the stage of the ongoing outbreak and implement more frequent twice-weekly testing in the context of escalating outbreaks and less frequent once-weekly testing when the transmission has slowed.
Refer to the CDC’s Performing Broad-Based Testing for SARS-CoV-2 in Congregate Settings for more information.
PCR is generally used for outbreak response testing, including mass testing. Antigen POC testing can be used if the number of tests needed is manageable, turn-around times for PCR are too long for the situation, and/or to target test those with the highest risk to get a quick estimate of the extent of the outbreak.
When testing is performed, a negative test only indicates that an individual did not have a detectable infection at the time of testing; individuals might have a COVID-19 infection still in the incubation period.
See the Recommended Respiratory Viral Testing by Clinical Presentation, Including Confirmatory PCR Testing table (Table 6.1) and Confirmation of COVID-19 POC (Rapid Antigen) Testing for information on when confirmatory PCR testing is needed for POC testing.
Testing must be accompanied by operational plans for use and follow-up of test results, including:
- How patients will be educated about why testing is being done (see the patient education materials located in the Patient Education tab on the COVID-19 webpage – CDCR networking is required for access).
- How patients who choose not to be tested will be managed
- How individual results will be explained
- How results will be used to guide the implementation of infection control measures: isolation, quarantine, and cohorting
- How results will be communicated to ensure appropriate management when inmates are released or transferred
Test all contacts (people who may have been exposed), if possible. An exposed contact is an asymptomatic person who may have had contact with a person who is a highly suspect case or a PCR-confirmed positive SARS-CoV-2 case and thus has the potential to become infected themselves. The more promptly this testing is done, the more likely the outbreak can be controlled.
If needed, testing can be prioritized as follows, in descending order: Exposure to a highly suspect or confirmed case includes but are not limited to:
- Close proximity to highly suspect or confirmed cases (<6 feet proximity for at least a cumulative time of 10 minutes or direct contact with secretions/being coughed or sneezed upon), regardless of whether the case and/or contacts were masked and outside of 90 days from a prior infection.
- Close exposures to the case:
- Cellmates or inmates in adjacent beds and cells in the same housing unit of a highly suspect or confirmed case or linkage to a high-risk group defined by public health during an outbreak (e.g., an affected dorm, housing unit, or yard).
- Sharing common spaces such as the yard, shower, dining hall, or day room and being in the same space for activities (e.g., work environments, in classrooms, groups, social activities, church, clinic visits, medication line, and commissary line) with highly suspect or confirmed cases.
Serial re-testing of housing unit inmates and others who are at potential exposure risk is necessary. See the section below on quarantine testing.
Consideration can be given to testing individual inmates at the highest risk of complications of COVID-19 based on underlying conditions and/or age. Inmates who test negative can be separated from the general inmate population to prevent becoming infected. Those who test positive should be isolated and closely monitored for progression of the illness.
COHORTS: COVID-19 MASS TESTING
Mass testing involves testing a moderate or large group of individuals suspected of having been exposed to COVID-19. Mass testing may include the entire institution, one or more yards, or one or more housing units. Workers with a common worksite exposure may also be tested as a group. Because mass testing helps determine the extent of transmission, it should also be used in areas not known to currently be involved in the active outbreak.
Inmates should be placed into separate cohorts based on exposure and test results. See Control Strategies for Suspected and Confirmed Cases and Control Strategies for Contacts to Cases sections.
Inmates are allowed to refuse to test. Inmates exposed in the previous 14 days need to be quarantined. If it is necessary to cohort quarantined inmates, the cohort should share exposure history and test outcome (negative versus refused).
Given the potential for high numbers of asymptomatic infections, ensure that plans include isolation options to house large numbers of infected individuals and quarantine options to house large numbers of close contacts, ideally separating exposure cohorts. Consider how the facility’s housing operations could be modified for multiple test result scenarios (e.g., if testing reveals that 10%, 30%, 50%, or more of incarcerated or detained persons test positive for COVID-19).
COVID-19 EMPLOYEE TESTING DURING OUTBREAKS
Integrating contact investigations and coordinating testing strategies amongst staff and inmates is imperative if successful disruption of viral transmission is to occur. For all situations that involve staff exposure, please contact Human Resources and the Office of Employee Health for further information/guidance. The CDCR Office of Employee Health Testing website can provide information on testing resources. Also see the COVID-19 Contact Tracing and Testing for Employees and Establishment of a Statewide Employee Health Program memos.
COVID-19 TESTING OF EXPOSED QUARANTINED PATIENTS AND PRIOR TO RELEASE FROM QUARANTINE
Patients who develop symptoms while in quarantine should be immediately isolated in a single cell with a solid walls and a solid door while awaiting test results.
Asymptomatic patients who have been exposed to COVID-19 should be offered viral testing, minimally, at the beginning (within 24 hours if they have not been tested within the last 7 days, or at 3 days post exposure), middle, and end of quarantine. If they test positive, they need to be removed from quarantine and isolated.
Because test sensitivity is imperfect, clinical judgment is essential in interpreting negative test results and discerning if additional testing is indicated. This is especially the case in high-risk exposures or exposures to persons at high risk of transmission to others (e.g., aerosol-generating procedures [AGPs] or job type).
Exposed patients who initially test negative shall be re-tested every 3-7 days. The specific re-testing interval that a facility chooses should be based on the stage of the ongoing outbreak (i.e., more frequent testing in the context of escalating outbreaks, less frequent testing when the transmission has slowed) and the risk level of the exposure (more frequent for higher risk exposures). Please refer to the Control Strategies for Contacts to Cases for more information on quarantine for case contacts.
Quarantine testing of exposed persons with POC antigen tests may be useful in some situations if immediate results are necessary, and PCR turn-around times are too long. Please refer to the section above on when confirmatory testing for POC should occur. Use only PCR when testing for release from quarantine.
For asymptomatic contacts of cases, follow up of negative POC tests with PCR is not generally necessary. However, if there is a clinical suspicion that the patient is infected, using PCR to confirm a negative POC is indicated.
Testing is also required to be released from quarantine. No sooner than quarantine day 12 of 14, and within 2 days prior to release, all patients shall be tested with PCR and have a negative result. Patients may refuse, but their quarantine time will be extended. For more details, please see the Control Strategies for Contacts of Cases section, the Release from Quarantine subsection, the Release from Quarantine Algorithm (Figure 13.1), and the last page of the Movement Matrix (Appendix 13) for more information. You may also request access to the COVID Transfer Registry to view patients’ isolation/quarantine status (CDCR networking is required for access).
Exposed Individuals <90 days from Prior COVID-19 Infection
The only persons who do not require testing when exposed are individuals who are within 90 days of their prior infection.
5. ROUTINE AND SURVEILLANCE COVID-19 TESTING AMONG ASYMPTOMATIC AND NON-EXPOSED PATIENTS
There are many situations where testing of asymptomatic, non-exposed persons will occur such as for high-risk patients, transfers and jail intakes, and surveillance testing. These testing recommendations provide strategies for monitoring potential transmission in asymptomatic, non-exposed persons. The goal of this asymptomatic monitoring is to prevent population transmission and to prevent individual morbidity and mortality through early identification and isolation of unrecognized COVID-19 cases.
ROUTINE TESTING OF NON-EXPOSED ASYMPTOMATIC PATIENTS AT HIGHER RISK OF COVID-19 MORBIDITY AND MORTALITY
- In general, PCR can be used for routine testing of high-risk patients. The rapid POC test may be useful when a result is needed urgently, and PCR turn-around times are too long.
- Routine testing among asymptomatic patients is recommended for those using AGPs such as nebulizers or continuous positive airway pressure (CPAP); repeat or serial testing may be valuable for patients with ongoing risk. This is particularly important if the areas in which these devices are used cannot be adequately ventilated or cleaned. In addition to routine serial testing, antigen POC testing may be used immediately before procedures. The higher the risk, the more frequently the testing should occur.
- Consider routine (e.g., at least monthly) testing for patients aged 65 or older or with medical comorbidities that put them at risk for complications of COVID-19 (see Table 5.3 and the COVID-19 Risk Registry – CDCR networking is required for access).
- Similar to the community, patients should be able to request COVID-19 testing regardless of symptom status.
ROUTINE COVID-19 TESTING OF INMATE WORKERS
CDC recommends expanding COVID-19 surveillance testing for workers in high-density worksites, worksites with large numbers of close contacts, and in healthcare and correctional environments.
Inmate workers in job categories with higher than average COVID-19 case rates in CCHCS are recommended to have routine weekly testing.
Leadership in each institution should review local healthcare and institutional operations and Prison Industry Authority (PIA) industries and identify inmate workers and worksites that may be at higher risk of infection or transmission, including those who work in:
- Enclosed spaces with employees or in areas where employees congregate
- Enclosed spaces with inmates outside of their housing unit
- Healthcare or other areas where patients are quarantined or isolated for COVID-19 or receive care
- Jobs that provide health aid or peer support for inmates with disabilities or other assistance needs
- Jobs that require movement about the facility or institution
The following inmate workers should be offered weekly viral testing unless previously recovered from COVID-19 (within 90 days of first the positive test):
- Culinary workers, including in kitchens, food preparation areas, scullery, and dining rooms
- PIA workers, including in manufacturing or fabrication, food processing or packaging, fabric products, and health facilities maintenance custodial assignments
- Workers in Correctional Treatment Centers (CTC), Skilled Nursing Facilities (SNF), and other healthcare environments, including all workers in the three SNF institutions (CCWF, CHCF, CMF)
- American with Disabilities Act (ADA) workers and others (including voluntary) who provide health aid or peer support (e.g., mental health, recreational), and Inmate Advisory Council members working outside of their housing units
- Porters, janitors, and clerks working in locations where employees work or congregate outside of their housing units
- Plant operations workers in enclosed spaces with others (e.g., warehouses, tool rooms, garages)
- All inmate workers should be screened for symptoms consistent with COVID-19 before leaving their housing units to report to the worksite as described in the Screening of Critical Inmate Workers memorandum (CDCR networking access is required).
COVID-19 TESTING OF TRANSFERS
Transfers to and from the institution may increase the risk of introduction and spread of COVID-19 between facilities. The COVID Screening and Testing Matrix for Patient Movement (Appendix 13) provides additional specifications on the testing strategy, housing, and what to do if the patient refuses to test. You may also request access to the COVID Transfer Registry to view patients’ isolation/quarantine status (CDCR networking is required for access).
COVID-19 TESTING OF EXPEDITED RELEASES/PAROLEES
COVID-19 PUBLIC HEALTH SURVEILLANCE TESTING
Surveillance testing is used to determine the extent of active infection in a population and to detect outbreaks in an early phase, even before developing symptoms. Early detection and rapid outbreak response can limit the spread of infection and prevent morbidity and mortality. Additionally, with sufficient numbers of appropriately selected patients testing negative, an institution can demonstrate with some confidence, the absence of an outbreak. PCR is preferred for surveillance testing.
The public health surveillance sample described below is appropriate for institutions (or parts of institutions) that are not responding to outbreaks or known exposures.
How Many to Test for COVID-19 Surveillance
Public health surveillance testing using PCR should be conducted weekly. Each cohort of patients at the prison that regularly commingles or shares airspace should be identified and have a sample tested each week. Depending on custody factors and the built environment, a cohort could consist of a single housing unit, a group of housing units on the same yard, or an entire yard. Using the following principles to guide the selection of patients for surveillance testing:
- For cohorts with 100 or more susceptible patients, test 25 patients each week. A sample of 25 patients will allow detection of a prevalence of 10% with 92% confidence.
- For cohorts with fewer than 100 susceptible patients, test 25% of the susceptible population each week.
- If there are multiple housing units with significant numbers of susceptible patients within a cohort, patients from each unit should be tested. In other words, do not select the entire sample from a single housing unit.
- Except for patients who are within the first 90 days after their first confirmed COVID-19 infection (early resolved period), all patients are considered susceptible for the purposes of surveillance testing. However, in the surveillance program, patients who are immunologically naïve (no history of COVID-19 infection or vaccination) should be the first priority for sampling since they are the most likely to become infected if exposed. Patients who are more than 180 days from their first infection should be the second priority for testing after the immunologically naïve.
- Testing of quarantined patients does not count toward the surveillance target in a cohort. Quarantined patients are not regularly comingling with the non-quarantined population, and therefore are not an appropriate sample.
- Surveillance testing of workers in a cohort does count toward the surveillance target of 25 (or 25%).
- Other testing of non-quarantined, asymptomatic, susceptible patients in the cohort may count toward the surveillance target of 25 (or 25%).
6. CONCERN FOR COVID-19 FALSE-POSITIVES: WHAT TO DO
All viral testing has the potential for false positives and false negatives. False positives can occur among patients with no history of COVID-19 as well as patients who have recently resolved infections (<90 days) and patients with more distant infections (>90 days prior). False positives have been documented for both the COVID-19 point of care antigen tests and the Quest RT-PCR test. Please note there is a difference between a false positive test result and a positive that reflects non-infectious shedding (true positives that are not clinically significant).
Being in a congregate setting, we must be conservative in our policy toward potential false positives. The CDPH (July 2020) supports the policy that at CDCR, every positive viral test should be treated as a true positive unless proven otherwise. Our setting and its extremely high risk of widespread transmission requires us to be more conservative regarding false positives.
The determination that a test was a false first positive or false re-positive, and the patient is NOT infected with COVID-19, should only be made after a thorough investigation. Hence, all patients with positive tests, even if suspected of being a false positive, must be isolated with full isolation PPE used, have twice-daily medical monitoring, and have a contact investigation conducted immediately. Close contacts should be quarantined and tested.
A positive result is more likely to be a false positive when there has not been an exposure and the patient is asymptomatic. Below details the information that should be considered when trying to determine if a positive test is actually a false positive:
- The patient is asymptomatic when tested and remains asymptomatic
- The patient has no known exposures and was not in quarantine for suspected exposure
- PCR testing of contacts reveals no other positive cases
- Subsequent PCR testing of the patient is negative
- Confirmatory samples should be sent as soon as possible from the first positive in question
Any patients with symptoms and a positive test is unlikely to be a false positive.
If an individual does not meet the criteria above, treat as a first-time infection in a COVID-19 naïve patient or follow the instructions for re-infections if the result is a re-positive after prior infection.
- Whether the test result in question is for a first-time positive or a re-positive, the patient must remain in isolation with full isolation PPE, continue with twice-daily medical surveillance, and the contacts remain in quarantine and continue quarantine testing while the steps are taken to investigate.
IF YOUR PATIENT IS DEEMED A FALSE POSITIVE:
- The evidence for the false-positive test result needs to be clearly documented in the chart.
- The supporting evidence for the false positive must be documented in the medical record by the Chief Medical Executive (CME), Chief Physician and Surgeon (CP&S), or designee. If the designee is the Primary Care Provider (PCP), the note must be sent for co-signing by the CME or CP&S.
- The correct result needs to be entered into SharePoint by the institution Public Health Nurse (PHN) – see Appendix 5).
- The patient may be released from isolation to the general population.
- The patient will not start a 90-day period of presumed immunity and should be considered susceptible to infection.
- The patient should participate in all testing programs and be quarantined if exposed.
7. RE-TESTING PREVIOUSLY POSITIVE PATIENTS AFTER RECOVERY FROM COVID-19
SUMMARY OF LITERATURE ON COVID-19 VIRAL SHEDDING AND RE-INFECTIONS
Although there are scattered events reported, there are currently only 5 confirmed cases of COVID-19 re-infection worldwide. Below details a summary of the CDC analysis and literature review on this topic.
Many studies show viral shedding to be prolonged after the resolution of symptoms of COVID-19, in some cases, as long as 60 days from symptom onset (median 31 days). Recovered patients can have COVID-19 RNA detected in their respiratory secretions for up to 90 days.
However, detecting viral RNA via PCR does not necessarily mean that an infectious virus is present. Viral shedding studies show that prolonged shedding is not likely to be infectious.
CDC analysis and literature review shows that viral shedding beyond 9 days from the onset of symptoms has not been grown in viral culture, except in immunocompromised patients with severe COVID-19. But even in these patients, 88-95% of specimens were no longer replication-competent after 10 and 15 days respectfully.
After 2 weeks of symptoms, the viral load found is orders of magnitude less than that in the first 5 days.
The statistically estimated likelihood of recovering a replication-competent virus approaches zero by 10 days from the onset of symptoms, if immunocompetent.
Also, as the likelihood of isolating replication-competent virus decreases, anti-COVID-19 IgM and IgG can be detected in an increasing number of persons recovering from the infection.
Concentrations of COVID-19 RNA in respiratory secretions decline after the onset of symptoms. Among those who continue to have detectable RNA, concentrations of detectable RNA 3 days following recovery are generally in the range at which replication-competent virus has not been reliably isolated by the CDC in unpublished data.
Infectious virus has not been cultured from urine or reliably cultured from feces in multiple studies; these potential sources pose minimal, if any, risk of transmitting infection, and any risk can be sufficiently mitigated by good hand hygiene.
A large contact study demonstrated that high-risk household and hospital contacts did not develop the infection if their exposure was 6 days or more after the case-patient’s symptom onset.
A Korean investigation reported by the Korean CDC of 285 “persistently positive” persons, which included 126 persons who had developed recurrent symptoms, found no secondary infections among 790 contacts attributable to contact with these case-patients. Efforts to isolate replication-competent virus from 108 of these case-patients were unsuccessful.
Despite some studies showing antibodies quickly declining, the scientific consensus is that immunity lasts at least 3 months. Cellular immunity is shown to be involved. An unpublished report of 20,000 people finds that 90% of antibody responses lasted at least 3 months.
Hence, after a review of the available literature, CDPH has responded with the following policy:
Previously positive COVID-19 patients (inmates and employees) who have recovered require re-testing when (includes all prior-to-infection testing including pre/post movement or transfers and quarantine/targeted housing/serial/mass/and surveillance testing):
- The time elapsed since the onset of the prior infection’s symptoms (or the time since the first positive test if asymptomatic) is >90 days.
- The time since the onset of the prior infection’s symptoms (or the time since the first positive test if asymptomatic) is <90 days, and the patient develops new symptoms.
All cases of new positives (POC or PCR) with symptoms, regardless of how long ago the patient recovered from their initial infection, are considered re-infections until proven otherwise and must be isolated using full isolation PPE, undergo twice-daily medical monitoring, have contact investigations started, and contacts put into quarantine.
Asymptomatic patients beyond the 90-day timeframe and newly test positive (POC or PCR) are also considered potential re-infections. They must be isolated using full isolation PPE, undergo twice-daily medical monitoring, have a contact investigation, and have close contacts quarantined and tested.
POTENTIAL COVID-19 RE-INFECTIONS
Patients being worked up for re-infection should remain in isolation, use full isolation PPE, have twice-daily medical monitoring, complete the contact investigation, and contacts should remain in quarantine and tested as close contacts.
The following factors should increase the suspicion for re-infection:
- The patient has new symptoms consistent with COVID-19.
- The patient tests positive by RT-PCR more than 90 days from their first positive test
- The patient had a known exposure in the past 14 days.
<90 Days Symptomatic Potential COVID-19 Re-Infections:
Symptomatic patients <90 days out with a positive POC or PCR is a situation more concerning for a false positive or it may be due to non-infectious shedding. These patients should:
- Have confirmatory PCR if the first test is a POC.
- Have other causes for the symptoms investigated.
- Be evaluated for other respiratory pathogens, and a comprehensive viral panel ordered.
If there is concern that the positive test is a false positive, follow the guidance on false positives in Concern for COVID-19 False-Positives: What to Do.
>90 Days Symptomatic Potential COVID-19 Re-Infections:
Symptomatic patients >90 days out also need to:
- Have confirmatory PCR (if not done/prior test is POC).
- Patients with a positive POC and negative RT-PCR cause concern for a false negative PCR because POC detects virus at a much higher threshold than PCR, and the non-infectious shedding period is presumed to be over. Repeat another RT-PCR in this circumstance.
- Have other causes for the symptoms investigated.
- Be evaluated for other respiratory pathogens, and a comprehensive viral panel ordered.
Then follow the directions in Studying Re-infections.
<90 Days Asymptomatic Potential COVID-19 Re-Infections:
Patients without symptoms within 90 days of their prior onset of symptoms (or first positive if asymptomatic) should not be tested. During this time frame, re-infections are highly unlikely and are considered false positives, and the test result may be disregarded.
>90 Days Asymptomatic Potential COVID-19 Re-Infections:
Asymptomatic patients >90 days out with a new positive:
- Should have two positive RT-PCRs for re-infection to be in the differential.
- Do not require other pathogen testing.
Consider if the result could be a false positive. See considerations for when a result might be a false positive in Concern for COVID-19 False-Positives: What to Do.
CDPH Studying COVID-19 Re-Infections and Re-Positives:
Whether re-positives are actually re-infections is of scientific interest and has a bearing on public health policy. The emergence of variant strains of the SARS-CoV-2 virus is concerning and potentially could be a cause of an increase in true re-infections. The CDPH viral lab may be able to support viral culture testing and whole genomic sequencing of suspected re-infection cases, especially if symptomatic. The CDPH criteria for further investigations are in flux, and as such, the PHB and CDPH are in constant communication regarding cases of interest and cases meeting the most recent CDPH criteria. In evaluating certain re-positive cases, PHN or Infection Control Nurse (ICN) completion of the secondary transmission and exposure information is important for understanding the context of re-positive cases and may be requested on a case-by-case basis.
Patients for whom CDPH opts not to pursue further testing should continue to be considered presumed re-infections, be isolated, and have twice-daily medical monitoring.
If there is any concern the result is actually a false positive, see the Concern for COVID-19 False-Positives: What to Do section.
If you have a re-positive patient who is >90 days out, whether symptomatic or asymptomatic, or a re-positive patient <90 days out with COVID symptoms, please do the following:
- Continue isolation using full isolation PPE, undergo twice-daily medical monitoring, have a contact investigation, and have close contacts quarantined and tested, as for all infections.
- Confirm any positive POC with a PCR as soon as possible.
- Ensure other causes for the symptoms, if present, have been investigated. If indicated, order a comprehensive viral panel or diagnostics for other pathogens.
- If a re-positive patient is symptomatic with classic COVID-19 symptoms and hospitalized, a re-positive case appears to be an index case for secondary transmission, or patients otherwise highly suspected of re-infection, please email an alert to the PHB (CDCRCCHCSpublichealthbranch@cdcr.ca.gov).
The PHB will contact Quest to hold the sample, try to obtain a cycle threshold, and pursue viral culture and genomic sequencing for specimens meeting the most updated CDPH criteria.
8. INFLUENZA VIRAL TESTING
Please refer to the Recommendations for Influenza and Other Respiratory Virus Testing and Reporting – 2020-2021 for detailed information on testing and reporting from CDPH.
Diagnostic testing of symptomatic persons is the only necessary testing for influenza. Symptomatic cases of ILI also need to be tested for COVID-19. While awaiting test results for both pathogens, patients should be isolated in single cells with doors that close.
Symptomatic patients are allowed to refuse testing but will still need to be isolated and complete the criteria defined in Release from COVID-19 isolation (not influenza).
Testing of asymptomatic people (e.g., contacts of influenza cases or mass testing) for influenza is not needed. Test only when symptomatic.
INFLUENZA TEST TYPES
See Appendix 19 for details on test ordering, collection, and laboratory details.
Quest Influenza NAAT/PCR
- Test symptomatic patients for influenza and COVID-19. Use PCR for influenza testing exclusively until the beginning of the annual influenza season. PCR can always be used for influenza.
- Follow Quest ordering information in Appendix 19.
Rapid Influenza Diagnostic Testing (RIDT)
Antigen testing (rapid influenza diagnostic testing (RIDT) can also be used for influenza testing once flu season 2020-21 arrives and/or the prevalence of influenza is designated by CDPH as “Local” or higher (See CDPH Weekly Influenza Surveillance Reports). Please refer to the Quidel Sofia2 SARS + Flu Antigen information website and the Quidel Sofia 2 device information webpage for detailed information.
Confirmation of Influenza Rapid Antigen Testing
Positive RIDT (when prevalence is high) test results can be relied upon to be true positives and do not need PCR confirmation.
Due to unreliable sensitivity, if the RIDT result is negative, further testing is always indicated. Order the influenza A/B RNA Qualitative PCR with or without RSV or other pathogens depending on the clinical scenario.
Please refer to Appendix 19 for order information.
Influenza Serology (Antibody) Testing
At this time, serology testing for influenza is not clinically used. Its main role is in research and special situations during public health investigations.
INFLUENZA OUTBREAK TESTING
Typically, influenza testing increases when an outbreak has been identified. Sometimes in the past, once an outbreak is identified, or a certain threshold of cases per housing unit, influenza could be presumed for ILI cases and isolated and treated accordingly. This will not be possible in the setting of a COVID-19 pandemic.
Mass testing, quarantine testing, surveillance testing, and testing pre/post movement is not needed for influenza.
9. OTHER RESPIRATORY VIRUS TESTING CONSIDERATIONS
- Clinicians should use their judgment in testing for other respiratory pathogens, including tuberculosis (TB), RSV, and coccidioidomycosis (Valley Fever).
- The RSV season generally coincides with influenza season. RSV testing is indicated if it will affect clinical management. Consider testing for RSV in vulnerable populations, including those with heart or lung disease, bone marrow and lung transplant recipients, frail older adults, and those with multiple underlying conditions. More information can be found on the CDPH’s webpage on Influenza and Other Respiratory Pathogens.
- Patients with coccidioidal infection develop symptoms and detectable antibodies within 7-21 days of exposure. Patients who demonstrate measurable anti-coccidioidal antibodies are likely to have a recent illness or one that continues to be active because antibody levels decrease over time and eventually become undetectable in most patients who resolve their infection. More information can be found in the Cocci Skin Test (CST) Education and Cocci Surveillance Training Slides (CDCR networking is required for access to both), the CCHCS Cocci Care Guide, and the CDPH’s webpage on Valley Fever.
- For TB concerns, see the CDC on TB testing and the CDPH California Tuberculosis Controllers Association (CTCA) Joint Guidelines for Tuberculosis Diagnosis and Treatment, revised June 2019.