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3. Workflow and information management for COVID-19 (and other pandemics)

3.1 Laboratory informatics and workflow management

The following should be considered when selecting a laboratory information management systems (LIMS) or laboratory information systems (LIS) to assist COVID-19 and other respiratory disease testing workflow.

Does the system have a flexible provider portal?

What types of providers are ordering COVID-19 tests? From surgeons ordering for pre-operation procedures and emergency room physicians for ER patients, to pathology groups and home health care agencies ordering for their patients, a wide variety of provider types exist. Those provider types and their special needs should be addressed. For example, physicians of record for home health care clients may not only require support for digital signatures in portal order entry, but additional verbal authorization of the test may also be required. The system should have a means for ensuring and verifying these order entry components are present.

Does the system allow for flexible addition of providers and patients?

Lab: Roles set by location, granular based on location

Include patient history notes that help indicate the need for testing (body temperature, patient symptoms, travel history, existing health conditions that could increase risk)

Does the system allow for workflows sympathetic to COVID-19 and other types of respiratory illness testing?

Orders - Test requests that have not been managed by the lab yet - Click Receive Order to actually receive the unstarted test. Sample batch - Batching = steps in the workflow ; can be client-specific broken-down steps or just a single prep step; depends on lab's workflow

• Can assign instruments to batch/workflow steps
• Can add QC or duplicate samples as part of the batch

Data entry - Shows assigned tests, and the associated samples assigned to the tests

• Can have assigned default or "Starter" values, e.g., "negative" result or null
• Approve tests/samples in a batch/workflow step before they move into the next batch/workflow step (ensure analysts are approving)
• Approve all samples in a batch, receiving warning if results are out of spec

Configurable sample type (swab, blood, saliva, etc.) and container types (sterile container/viral transport media or container with saline)

Link a department to a test type, e.g., serology, pathology, etc.

Rapid COVID workflow (molecular) 1. Batching 2. Batch plating 3. Extraction 4. qPCR Plate 5. Analysis 6. Review

COVID-19 IgG and IgM Duo (serology)

Does the system allow for interfacing with most instruments currently testing for COVID-19?

Instrument management - Interfaces set up with newest POC instruments etc. and have specific tests assigned to instruments

Does the system allow for flexible viewing and reporting of COVID-19 results? Pathologist provides consultation notes on final report, they look at results and give clinical and diagnostic guidance based on those results Usually comes in with a preliminary final report - Have an extra step where the report received comments from pathologists or NP.

Report review and appoval - Reflex testing: Presumptive positive for COVID-19, confirmation tests are automatically added

Disease- or test-specific dashboard - Show all samples related to test, positives, negatives, pending results, tests per day, etc.

3.2 Laboratory informatics and reporting requirements

Epidemiology can broadly be split into two categories: descriptive epidemiology and analytical epidemiology. Descriptive epidemiology involves studies and other activities that deal with geographical comparisons and temporal trend descriptions of disease. As such, the collection and use of quality incidence data is vital to developing hypotheses. Analytical epidemiology allows for the testing of those hypotheses using both experimental and observational studies, as well as control groups. Similarly, the collection and use of quality experimental and observational data is vital for proving or disproving hypotheses. In both cases, proper reporting of public health data is critical to the success of epidemiologists' response to outbreaks and pandemics, as well as the credibility of their research.

The proper reporting of COVID-19 case data is no exception. In the United States, the Centers for Disease Control and Prevention (CDC) has taken a standardized approach to collecting reports on "individuals with at least one respiratory specimen that tested positive for the virus that causes COVID-19." Their COVID-19 Case Report Form is designed to collect a wide variety of information about a COVID-19 case, including patient demographics, epidemiological characteristics, exposure and contact history, and clinical diagnosis and treatment procedures. Currently, the CDC is asking local and state health departments to submit case reports, and asking healthcare providers and laboratories to contact those health departments when "concerned that a patient may have COVID-19." The CDC has also slimmed its reporting requirements, limiting reporting of "persons under investigation" to areas where testing must be forwarded to the CDC due to insufficient capacity to test locally. Electronic reporting using the CDC's system is preferred, but they have a protocol for those areas unable to submit electronically. Canada has similar reporting expectations, with their own case report form and electronic data submission process through the Public Health Agency of Canada. And in the European Union, member countries and the U.K. are asked to report through the Early Warning and Response System.

3.2.1 ICD and CPT coding

Related are any internal reporting requirements, particularly for test reporting in labs and medical facilities. (And in some cases, reporting to local health departments requires additional internal reporting adjustments). The International Statistical Classification of Diseases and Related Health Problems (ICD) is a commonly used system of diagnostic codes for classifying diseases, including nuanced classifications of a wide variety of signs, symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or disease. Their ICD-10-CM code set has been modified to include lab testing codes for COVID-19, as has the Current Procedural Terminology (CPT) code set. This guide provides basic information about these codes (which should not be considered legally binding advice); however, see the referenced material (and following citations) for more details concerning those codes:

• The CPT code 87635 has the long descriptor of "Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease [COVID-19]), amplified probe technique." The American Medical Association's CPT Assistant fact sheet for SARS-CoV-2 reporting proves useful in supplying assistance on how and when to apply this CPT code in reporting.

• The U.S. government-adopted ICD-10-CM—an authorized version of WHO's ICD-10—has been updated by the CDC and the National Center for Healthcare Statistics. It includes not only new codes for conditions associated with COVID-19 but also codes for exposure and screening. The principal diagnosis code "U07.1, COVID-19" is sequenced first, followed by any appropriate codes for associated manifestations (though there is an obstetrics exception). The CDC's official coding guidelines, as well as guidance from Dr. Erica Remer may prove useful in choosing the correct codes.

Laboratories analyzing specimens for SARS-CoV-2 must be equipped to implement and handle analytical testing and test orders using the new test codes. However, they also must be able to quickly and accurately transfer vital case information to the appropriate health authority.

3.2.2 Reporting to local and regional health departments

Given the valuable nature of case reports during an epidemic, health care providers, facilities, and laboratories are being held responsible for sending case data to their local and regional health departments. That information then feeds up to the state-level health department, which then makes its way to the national-level entity responsible for handling epidemiology (in the case of the U.S., the CDC). However, the general disease reporting requirements vary from state to state, with some states encouraging full electronic laboratory reporting (ELR), while others still encouraging faxed or mailed reports. Add in the urgency and confusion associated with a pandemic, and COVID-19 reporting requirements prove to vary just as much. Some states' health departments have taken a proactive approach to reporting. For example, Iowa's Department of Public Health has issued several mandatory COVID-19 reporting orders meant to supplement existing reporting rules, including an order requiring all Iowa health care providers and public, private, and hospital laboratories "to immediately report all positive and negative Coronavirus Disease 2019 (COVID-19) testing results to the department." Other states have not been as clear on their reporting requirements, in some cases not having any guidance documents or clear information on their health department website for how providers, facilities, and labs should report COVID-19. In those cases, the presumption is that most labs have contacted the health department for advice or are reporting COVID-19 cases as immediately reportable, based upon the state's existing reporting requirements for immediately reportable diseases.

Table 1 addresses the reporting requirements for the United States' 50 states, while Table 2 covers U.S. territories. If clear reporting guidance specific to COVID-19 could be found, it was described. If no such guidance could be found, then the state's existing guidance and rules regarding disease reporting were referenced. In some cases, the state health departments don't clearly spell out whether a faxed or mailed report is required after immediately phoning in a report. In other cases, it's not clear if ELR—though it exists—is an acceptable form of reporting COVID-19 cases. This ambiguity is stated in the form of a "(?)" found next to the "Y" and "N" for electronic filing and faxing. In all cases, if there is any doubt about reporting requirements, call your local health department to confirm.

Table 1. U.S. state-based COVID-19 reporting requirements State Electronic file (Y/N) Fax? (Y/N) Forms for reporting Contact Additional details Alabama Y N Novel Coronavirus Report Form ALNEDSSsupport@adph.state.al.us "Providers who are either reporting laboratory results for patients tested by a commercial or clinical laboratory (not tested by the BCL) or reporting deaths among patients with positive results must complete" the report form. "Laboratories are required to report all negative and positive COVID-19 virus test results electronically (faxes do not count). If not already enrolled, laboratories will need to manually enter test results directly into the surveillance system." Email the contact to enroll staff access to the system. Alaska Y Y Confidential Infectious Disease Report Form COVID Reporting Hotline: 1-877-469-8067   Urgent situation: 907-269-8000 or 800-478-0084 (after-hours)   ELR: megan.tompkins@alaska.gov "Providers must report laboratory-confirmed cases of COVID-19 to SOE by either leaving a message on the COVID Reporting Hotline (1-877-469-8067) or via fax using the standard Infectious Disease Report Form." "[A]ll results both positive and negative must be reported via either integration into existing electronic laboratory reporting (ELR) data feeds or fax (907-563-7868). Please email Megan Tompkins ... to inform us about how your facility will report." Arizona Y Y Sample Aggregate Weekly Submission Form Sample ADHS CSV File Sample ADHS Excel File Fax: (602) 364-3199   ELR: elr@azdhs.gov "[A] laboratory as defined in A.R.S. § 36-451(4) shall report all COVID-19 test results (positive and negative) to the Arizona Department of Health Services in an electronic format as follows: a. For laboratories reporting to the Arizona Department of Health Services through electronic lab reporting ('ELR'), results of all COVID-19 tests; b. For laboratories not reporting to the Arizona Department of Health Services through ELR, a weekly aggregate number of total COVID-19 tests performed and their results." If reporting is accomplished through mail or fax, use the Sample Aggregate Weekly Submission Form. "Aggregate reporting does NOT replace mandatory laboratory reporting requirements per Arizona Administrative Code R9-6-204."   "ADHS has created a new electronic option for reporting results of COVID-19 in-house testing as an alternative to Health Level Seven (HL7) electronic laboratory reporting or direct entry into MEDSIS. This can now be accomplished through a standardized spreadsheet or comma separated value (CSV) file format." Arkansas N Y (?) Communicable Disease Reporting Form Phone: (501) 537-8969 or 1-800-554-5738 after-hours Arkansas Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating "suspected or confirmed" COVID-19 cases as an immediately reportable event that "are to be reported immediately to the ADH," via telephone. The language used on its reportable disease instructions suggests that a follow-up fax of the case report isn't required; however, call and confirm with the DoH. The DoH disease reporting web page makes no mention of ELR. California Y N (?) Confidential Morbidity Report Contact: Local health officers   CalREDIE: CalREDIEHelp@cdph.ca.gov or (866) 866-1428 The DPH has added COVID-19 to its Reportable Diseases and Conditions lists for health care providers and laboratories. This health care provider document indicates that a "case or suspected case" of COVID-19 should be reported immediately by phone. The document makes no mention of requiring a follow-up fax or digital report by health care providers. The laboratory document indicates "[l]aboratories must report any initial findings as well as any subsequent findings. ”Any laboratories approved to test for SARS-CoV-2 must report all positive and non-positive (negative, indeterminate, and specimen unsatisfactory) test results from both antigen/molecular and antibody/serology tests for SARS-CoV-2." Laboratory findings are "are reportable to the local health officer of the health jurisdiction where the patient resides by telephone within one (1) hour ... from the time that the laboratory notifies the health care provider or other person authorized to receive the report." Labs are asked to also subsequently report results electronically (ELR) to the California Reportable Disease Information Exchange (CalREDIE) "within one working day of identification." Colorado Y Y General Communicable Disease Reporting Form Fax: (303) 782-0338   CEDRS: lavelle.fernandez@state.co.us   ELR: andrew.horvath@state.co.us The state doesn't appear to have specific rules or a reporting form for laboratory reporting of COVID-19. Presumably labs are reporting COVID-19 as is required for any communicable disease. The state lists multiple ways to report a case: calling, faxing a General Communicable Disease Reporting Form, through CEDRS, or by using ELR. They also offer guidance for healthcare providers. "Any suspected or confirmed case or outbreak of COVID-19 should immediately be reported to the local or state public health agency. To report, utilize the [Outbreak COVID-19 Outbreak Report Form]. Send this form to your local public health agency OR to CDPHE by securely emailing a completed form to: cdphe_haioutbreak@state.co.us." Connecticut Y Y 2019 Novel Coronavirus (COVID-19) Case Report Form   Reportable Laboratory Findings, Form OL-15C Fax: (860) 629-6962   ELR: dph.elr@ct.gov Presumably labs are reporting COVID-19 as is required for any communicable disease. This has traditionally been done using Form OL-15C sent through mail or fax, as well as ELR. "Providers can now submit a COVID-19 case report online. This is the preferred way to submit COVID-19 case reports." Delaware Y N No standardized COVID-19 reporting form Call: 1-888-295-5156   Email: reportdisease@delaware.gov "COVID-19 is a reportable condition to the DPH. Any positive test results from any laboratory must be reported to DPH via the Delaware Electronic Reporting Surveillance System (DERSS). If you have a strong clinical suspicion that a patient may be infected with COVID-19 based on clinical symptoms and epidemiological factors (e.g., close contact with a confirmed case, recent travel to an area with sustained transmission), contact the DPH Office of Infectious Disease Epidemiology at 1-888-295-5156, or report through reportdisease@delaware.gov within 24 hours leading to submission of test samples to a commercial lab to allow for surveillance and monitoring as appropriate." The state makes no mention of reporting negative COVID-19 test results. District of Columbia N Y No standardized COVID-19 reporting form Phone: (202) 442-8141 or 1-(844)-493-2652 after-hours   Fax: (202) 442-8060 DC Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating COVID-19 tests with "provisional diagnosis or the appearance of suspicious symptoms" as an immediately reportable event that "must be reported immediately by telephone ... and confirmed by submission of a case report within 24 hours." ELR appears to be reserved for specific diseases other than COVID-19. Florida Y Y No standardized COVID-19 reporting form Fax: (850) 414-6894   ELR: MUElectronicLabReporting@flhealth.gov or ELR@flhealth.gov "Commercial laboratory results for COVID-19 will either be reported through electronic laboratory reporting (ELR), faxing, or phone calls from laboratories. Results received at the Bureau of Epidemiology will be sent to counties via Merlin. Bureau of Public Health Laboratories test results are reported to [county health departments] through Merlin and they are mailed to the ordering providers." In separate documentation, the state notes that both positive and negative COVID-19 laboratory results should be reported. As for health care providers and facilities, they must report a [specific set of persons related to COVID-19 to the County Health Departments. Georgia Y Y Notifiable Disease Report Form   Notifiable Disease Reporting Requirements Fax: Based on District Health Office   Call: 1-866-782-4584 Georgia lists COVID-19 as an immeadiately reportable disease condition. "All Georgia physicians, laboratories, and other health care providers" are encouraged to call their District Health Office or the main number. The state is also accepting COVID-19 reports through its SendSS online application. Hawaii Y (?) Y Person Under Investigation (PUI) and Case Report Form Fax: (808) 586-4595   ELR: helpdesk@hawaiihie.org "Per the Hawaii Administrative Rules, Chapter 11-156, the Person Under Investigation (PUI) and Case Report Form must be completed for any person who tests POSITIVE for COVID-19. Please fax the completed form to the Disease Outbreak Control Division at (808) 586-4595. COVID-19 is considered an URGENTLY REPORTABLE condition." It's not entirely clear if laboratories can use ELR through the Hawaii Health Information Exchange for COVID-19 reporting. They simply state: "Results for patients who have been tested for COVID-19 are incorporated into their records in the HHIE Community Health Record." Idaho N Y No standardized COVID-19 reporting form Phone: (208) 334-5939   Fax: (208) 332-7307   ELR: PublicHealthMU@dhw.idaho.gov The Idaho Department of Health and Welfare doesn't appear to have published any information about COVID-19 reporting requirements. They simply state that "Labs will report their results to the state, and those numbers will be posted on this website each day." Presumably this means that labs should be following the state's reportable diseases protocol for reporting "within one working day of identification or suspicion" using phone or fax. No standardized reporting form appears to exist. It's not clear if ELR is being used to report COVID-19 cases. Illinois Y Y No standardized COVID-19 reporting form Fax: Based on Local Health Department   ELR: DPH.Helpdesk@illinois.gov or DoIT.Helpdesk@Illinois.gov The Illinois Department of Public Health doesn't appear to have published an information about COVID-19 reporting requirements. However, given their laboratory reporting requirements in general, COVID-19 is nearly certain to require "immediate" reporting, which to the state means within three hours. Its laboratory reporting requirements document recommends contacting the local health department to send the report. However, ELR through Illinois’ National Electronic Disease Surveillance System (I-NEDSS) appears to be the preferred method. Indiana Y Y Confidential Report of Communicable Diseases ELR: (317) 233-7684 or ijameson@isdh.in.gov   Fax: (317) 233-7747 "You should report both positives and negatives the same way you report all other reportable disease conditions to ISDH. This is primarily through electronic laboratory reporting (ELR) through the ISDH NBS system. If your facility currently reports labs through ELR to ISDH, contact Irene Jameson to set up COVID-19 reporting (317-233-7684 or ijameson@isdh.in.gov). If your facility does not currently report through ELR, please have your infection preventionist (IP) report through a morbidity report. Provide a pdf of the lab report to your IP as they will need to attach this file when submitting their report. ISDH is not onboarding new ELR/NBS customers currently. Alternatively, you can fax positive reports to 317-233-7747." Such reporting should be done within 24 hours of test completion. Iowa Y Y Disease Reporting Card ELR: Jill Newland   Fax: (515) 281-5698 "All Iowa health care providers and public, private, and hospital laboratories are required to immediately report all positive and negative Coronavirus Disease 2019 (COVID-19) testing results to the department. Reports must be made electronically through the Iowa Disease Surveillance System (IDSS) when a facility has electronic transmission capabilities, otherwise reports can be faxed to 515-281-5698." Kansas N Y Kansas Reportable Disease Form Phone: (877) 427-7317   Fax: (877) 427-7318 "COVID-19 is a reportable disease, so you must have a mechanism for reporting both positives and negatives to KDHE." However, the KDHE doesn't appear to have any additional laboratory reporting instructions for COVID-19. It's not explicitly clear, but the state is presumably treating COVID-19 as a four-hour (within four hours of test completion) reportable disease. According to its reportable diseases guidance: "For 4-hour reportable diseases report to the KDHE Epidemiology Hotline: 877-427-7317. For all other reportable diseases fax a Kansas Reportable Disease Form and any lab results to your local health department or to KDHE: 877-427-7318 within 24 hours or by the next business day." The KDHE disease reporting web page makes no mention of ELR. Kentucky N Y COVID-19 Person Under Investigation (PUI) Report Form   Kentucky Reportable Disease Form Fax: (502) 696-3803 "If the test result for COVID-19 is positive, please fax the completed PUI form to the KDPH secure fax line at 502-696-3803 along with the EPID-200 Reportable Disease Report Form." It's not clear if any COVID-19 reporting is being performed using ELR. Louisiana N Y Confidential Disease Case Report Phone: (504) 568-8295   Fax: (504) 568-8290 Louisiana's Emergency Rule - LAC 51:105 and 107 adds COVID-19 to Class A reportable diseases. "This Emergency Rule makes the reporting of COVID-19 cases mandatory for all healthcare providers. This Emergency Rule makes all laboratory tests for COVID-19, whether positive or negative, reportable to the State within 24 hours of test result." Class A diseases "of major public health concern" are apparently to be reported "by telephone immediately." The LDH disease reporting web page makes no mention of ELR. Maine N Y No standardized COVID-19 reporting form Phone: 800-821-5821   Fax: 800-293-7534 The Maine CDC doesn't appear to have published any information about specific COVID-19 reporting requirements. The Maine CDC is presumably treating COVID-19 tests that are "positive by any method" as an immediately reportable event "by telephone to Maine CDC." According to its guidance, it doesn't appear ELR is employed for immediately reportable events. Maryland N Y (?) Confidential Report: Laboratory Evidence of Certain Communicable Diseases Contact: Local health department The Maryland Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating COVID-19 tests with "a positive laboratory finding" as an immediately reportable event that "should be submitted to the local health department in the jurisdiction where the lab is located." It's not clear what the best method for reporting (phone, fax, ELR) is for COVID-19 positive results. Presumably labs should contact their local health department to confirm this. The DoH disease reporting web page makes no mention of ELR. Massachusetts N Y No standardized COVID-19 reporting form Contact: Local health departments   MDPH phone: (617) 983-6800   MDPH fax: (617) 983-6813 The State of Massachusetts doesn't appear to have published any information about specific COVID-19 reporting requirements. The state is presumably treating COVID-19 "suspected and confirmed cases" as an immediately reportable event that "should be reported to your local board of health" by phone, or if unavailable, to the Massachusetts Department of Public Health by phone or fax. The MDPH disease reporting web page makes no mention of ELR. Michigan Y Y No standardized COVID-19 reporting form MDSS: Support contacts   Contact: Local health department list in reporting guide The Michigan Department of Health & Human Services has updated its Health Care Professional's Guide to Disease Reporting in Michigan to include detections of SARS-CoV-2. They note that "if the agent is identified by clinical or laboratory diagnosis," the detection (by both healthcare providers and laboratories) "must be reported to the Michigan Disease Surveillance System (MDSS) or local health department within 24 hours." As for how: "Mandatory reporting of communicable diseases can (and, whenever possible, should) be accomplished via the MDSS. The MDSS is a web-based communicable disease reporting system developed for the state of Michigan." If unable to electronically report, contact the local health department using the directory in the disease reporting guide. Minnesota N Y COVID-19 Case Report Form Fax: (651) 201-5743   Phone: (651) 201-5414 or (877) 676-5414 "The Minnesota Department of Health (MDH) is requiring all mandated reporters to report any cases and deaths due to SARS-CoV-2 to MDH within one working day." This includes health care facilities, medical laboratories, and in special cases veterinary laboratories. Case report forms can be faxed or case reports submitted by phone. The MDoH disease reporting web page makes no mention of ELR. Mississippi Y (?) N Reportable Diseases and Conditions form Phone: (601) 576-7725 or 1-800-556-0003; for weekends, holidays and after 5pm: (601) 576-7400 The Mississippi State Department of Health states: "All COVID-19 results must be reported to the Mississippi State Department of Health at this time." However, it gives no further guidance specifically for commercial laboratories or health care providers testing for SARS-CoV-2. Presumably the MSDH is considering COVID-19 a Class 1A disease, required to be "reported directly to the Department of Health by telephone within 24 hours of first knowledge or suspicion." The MSDH also has an online disease reporting tool (account required); however, it's not clear if it is equipped to received COVID-19 reports. Missouri Y Y sFTP Excel template   Disease Case Report form sFTP: (573) 526-5271   Fax: (573) 751-6417 The Missouri Department of Health and Senior Services has officially added COVID-19 to its list of immediately reportable conditions, including a waiver "to require that all positive and negative results for COVID-19 are sent directly to DHSS. Now, all laboratories must report directly to DHSS." They add that "[l]aboratories are encouraged to report via electronic means ... by secure file transfer protocol (sFTP)." Alternatively, labs may also submit a report to the Bureau of Reportable Disease Informatics (BRDI) via fax. "[M]edical providers (non-laboratories) also have an obligation to submit disease case reports (form CD-1) to DHSS. However, under the current suspension, when the testing is conducted outside the hospital by a separate laboratory that must also report the result to the Department, only the laboratory must make the report." Montana N Y (?) No standardized COVID-19 reporting form Contact: Local health department   DPHHS phone: (406) 444-0273 The Montana Department of Public Health and Human Services doesn't appear to have published any information about specific COVID-19 reporting requirements. The state is presumably treating COVID-19 like its other reportable diseases: "whether suspected or confirmed" the case "must be reported immediately to your local health jurisdiction as required by the Administrative Rules of Montana." If the local public health jurisdiction is unavailable, a call can be placed to the MDPHHS. It is not clear if laboratories should report both positive and negative results, though news reports have shown that the DPHHS is reporting both positive and negatives. The disease reporting web page makes no mention of ELR. Nebraska N N Health Care Provider Confidential Communication form   Laboratory Summary of Reportable Diseases, Poisonings and Organisms Phone: Based on county The Nebraska Department of Health and Human Services provides little in the way of specific guidance for reporting COVID-19. They simply state: "Any patient (+) for COVID-19 virus should be immediately reported to local/state public health office." They define "immediate notification" as "required to call by telephone to a live public health surveillance official within 24 hours of detection." This apparently includes providers currently on ELR. Labs and healthcare providers should verify if any additional reporting (fax, ELR) is required. Nevada N Y Confidential Disease Reporting Form Contact: Local health department list in reporting form Nevada DHHS guidance states health care providers, medical facilities, and laboratories should immediately notify the head of infection control or laboratory director at their facility AND "their local/state health department in the event of a probable or confirmed case of COVID-19." Its guidance appears to suggest a phone call for such notification. According to the state's disease reporting form, this phone call should be done in addition to faxing a report. "All cases, suspect cases, and carriers must be reported within 24 hours." It's not clear if ELR is being accepted for COVID-19 reporting. New Hampshire N Y COVID-19 Case Report Form Phone: (603) 271-4496   Fax: (603) 271-0545 Health care providers and laboratories should immediately report suspect and confirmed cases of COVID-19 to the New Hampshire Department of Health and Human Services. It seems likely the DPHHS prefers both a phone call and a faxed report, though it's not explicitly stated. The case should likely be "reported within 24 hours of diagnosis or suspicion of diagnosis." The NHDHHS disease reporting web page makes no mention of ELR. New Jersey Y N (?) No standardized COVID-19 reporting form ELR: See quick-start guide   Local health departments "[T]he New Jersey Domestic Security Preparedness Task Force hereby directs that commercial laboratories operating in New Jersey report all COVID-19 test results to the New Jersey Department of Health beginning March 23, 2020. The results of all COVID-19 tests performed before this date shall be included in the initial report. Subsequently, results shall be sent daily, and included results not previously reported. Information shall be transmitted no later than 8:00 p.m. each day through the Department of Health’s CDRSS platform. Specific data reported shall include positive, negative, and inconclusive test results. This directive shall supplement, not supplant, any other existing reporting requirements." From that statement, it's not clear if laboratories should also be immediately phoning their results to the health department in addition to ELR over CDRSS. New Mexico N Y (?) Notifiable Condition Report Form Phone: (505) 827-0006   Fax: (505) 827-0013 The New Mexico Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating "confirmed or suspected" COVID-19 cases as an immediately reportable event that "require immediate reporting by telephone to Epidemiology and Response Division." It's not clear if a faxed report is also required. The DoH disease reporting web page makes no mention of ELR. New York Y N Confidential Case Report - DOH-389   Universal Reporting Form - PD-16 Contact: Local health departments   ECLRS: eclrs@health.ny.gov The New York Department of Health states: "Positive results must be immediately reported to the local Department of Health by the laboratory performing the test, per established guidance, and all test results should be reported by the laboratories into New York State Department of Health’s Electronic Clinical Laboratory Reporting System (ECLRS) four times a day." The established guidance appears to be found in the state's updated reporting instructions, which now includes COVID-19 as a disease that "should be reported immediately to local health departments by phone followed by submission of the confidential case report form (DOH-389). In NYC use case report form PD-16." This means "within 24 hours of diagnosis." The instructions indicate case reports should be mailed. Both health care facilities and laboratories should report. North Carolina N Y COVID-19 Confidential Communicable Disease Report Contact: Local health departments   Fax: (919) 733-0490 Per NCDHHS's clinical diagnostic laboratory guidance: "Immediate notification of the detection of COVID-19 should be sent to the Communicable Disease Branch fax at (919) 733-0490. Statistics on total COVID-19 tests completed, total negative tests, and total positive tests on a cumulative and 24 hours basis should be sent daily to SERT Emergency Services (NCEM) SERTEmergencyServices@ncdps.gov and SERTPLANS (NCEM) sertplans@ncdps.gov for statistical reporting." This is similar to April 20 guidance which claims that "physicians and laboratories in North Carolina are required to immediately report suspected or confirmed cases of novel coronavirus infection to state or local health departments via telephone or facsimile of basic contact information of the case." Ohio Y Y Ohio Confidential Reportable Disease form Contact: Local health districts   ELR: ELR@odh.ohio.gov In March 2020, the Ohio Department of Health ordered "confirmed cases of COVID-19 be reported immediately as a Class A disease pursuant to Ohio Adm. Code 3701-3-02(A) to the local health district in which the person resides (or the local health district wherein the person is being medically evaluated if the person's residence is unknown or not in Ohio)." Physicians, medical care facilities, and laboratories are encouraged to report positive cases. Per the state's communicable disease requirements, Class A diseases should be reported immediately by phone, with a follow-up HEA 3334 Ohio Confidential Reportable Disease form. That requirements doc also states " follow-up reports can also be made electronically through direct entry into the Ohio Disease Reporting System (ODRS) or through Electronic Laboratory Reporting." Oklahoma Y Y Reportable Disease Card for Healthcare Providers (Blue Card)   Reportable Disease Card for Laboratories (Yellow Card) PHIDDO: adservice@health.ok.gov   Phone: (405) 271-4060 Fax: (405) 271-6680   ELR: AnthonyL@health.ok.gov The Oklahoma State Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating "laboratory results indicating" (i.e., "upon suspicion, diagnosis, or positive test") COVID-19 as an immediately reportable event "to the OSDH by PHIDDO or telephone (405-271-4060)." This also holds true for healthcare providers. The Public Health Investigation and Disease Detection of Oklahoma (PHIDDO) system is apparently the preferred method, though other methods are acceptable. Oregon Y Y COVID-19 Report Form Contact: Local public health authority   Fax: (971) 673-1100   Online morbidy reporting or ELR: (971) 673-1111 "The Oregon Health Authority (OHA), Public Health Division, is temporarily adopting OAR 333-017-0800 and OAR 333-018-900, which adds a definition of COVID-19 and adds COVID-19 to the list of diseases reportable to public health authorities within 24 hours. Positive test results for COVID-19 must be reported within 24 hours and negative COVID-19 results within one working day." "Both medical laboratories and health care providers are required to report COVID-19 test results to the state and local public health authorities." According to state law, reports should be initially submitted by phone call, with a follow-up report either through the online morbidity report tool or a fax. ELR may also be an option. Pennsylvania Y N No standardized COVID-19 reporting form (use PA-NEDDS) PA-NEDSS: 1-877-724-3258 From the Pennsylvania Department of Health: "COVID-19 is a reportable condition to the DOH. Any positive test results from any laboratory must be reported to DOH via the Pennsylvania National Electronic Disease Surveillance System (PA-NEDSS)." COVID-19 is now on the list or reportable diseases, and it must be reported with 24 hours. Rhode Island N Y PUI for COVID-19 - Reporting Form Phone: (401) 222-2577 or (401) 276-8046 after hours   Fax: (401) 222-2488 Per the Rhode Island Department of Health: "Any suspected cases of COVID-19 should be reported to RIDOH immediately. For any questions and to report cases, please call the Rhode Island Department of Health Center for Acute Infectious Disease Epidemiology at 401-222-2577 during business hours (Monday – Friday, 8:30 a.m. – 4:30 p.m.) or 401-276-8046 after hours." Presumably a follow-up fax using the COVID-19 reporting form is also required. The report "must be reported on the day of recognition or strong suspicion of disease." The RIDOH disease reporting web page makes no mention of ELR. South Carolina N (?) N (?) No standardized COVID-19 reporting form Contact: Local public health office   ELR: 1-800-917-2093 Per the South Carolina Department of Health and Environmental Control: "If results were from a private lab, please notify DHEC of positive result. COVID-19 is an immediately reportable condition on the South Carolina List of Reportable Conditions." However, an April 22 update now lists it as "urgently reportable," meaning within 24 hours by phone. The SCDHEC disease reporting web page does mention ELR, though it's not clear if it can be used to report COVID-19 cases. South Dakota N Y South Dakota Confidential Disease Report (online/HTML) Phone: (605) 773-3737 or 800-592-1861   Fax: (605) 773-5509 "SD-DOH would like to remind medical providers, hospitals, and laboratories that cases of COVID-19, caused by the SARS-CoV-2 virus, are considered immediately reportable in South Dakota (under Coronavirus Respiratory syndromes)." The SD-DOH and the state laws don't make clear what reporting method is best for Category I diseases, only that they should be reported immediately. Under "how to report," they list, in order, online reporting, phone, fax, and mail. The SD-DOH disease reporting web page makes no mention of ELR (other than completing the online/HTML form). Tennessee Y Y Person Under Investigation (PUI) and Case Report Form Fax: (615) 741-3857   Phone: (615) 741-7247   ELR: ceds.informatics@tn.gov "Healthcare providers who receive positive COVID-19 test results on their patients or patients in their facility [should report]." "Laboratories performing COVID-19 testing should be reporting these results electronically via ELR or our emergency spreadsheet template. If you are a laboratory that needs to report via one of these methods, please email ceds.informatics@tn.gov." These entities "should report within 24 hours of receiving a COVID-19 diagnosis, positive lab report on a patient, and/or becoming aware of a suspected or confirmed COVID-19 associated death." "Please submit a PUI Form on all positive COVID-19 test results from commercial labs only; you do not need to submit further information on a lab result from the TDH Public Health Laboratory. Please include a copy of the positive lab result." The Tennessee Department of Health lists three reporting options: faxing the PUI form and positive lab report, phoning, and electronically (via Morbidity Reports or ELR). Texas Y Y Infectious Disease Report (Single case)   Infectious Disease Report (Multiple cases) Contact: Local health department   ELR: COVID‑19ELR@dshs.texas.gov "On March 24, 2020, Governor Greg Abbott ordered every public or private entity that is utilizing an FDA-approved test, including an emergency use authorization test, for human diagnostic purposes of COVID- 19, shall submit to DSHS, as well as to the local health department, daily reports of all test results, both positive and negative." The state lists novel coronaviruses as an immediately reportable event by phone. Although not explicitly stated, an Infectious Disease Report form may also be required after the phone call; verify with your local health department. ELR registration can be performed online. After online registration, "please send the name of your facility, email, and a good contact number to COVID‑19ELR@dshs.texas.gov to get your account created." Utah Y (?) Y Utah Public Health Confidential Morbidity Report Fax: (801) 538-9923   Email: reporting@utah.gov   Phone: 1-888-EPI-UTAH   ELR: edx@utah.gov The Utah Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating COVID-19 cases as immediately reportable events ("within 24 hours of a suspect diagnosis") for healthcare facilities and laboratories. Reports may be faxed (note that the "disease reporting fax line is an email fax"), emailed, or phoned. Emailed reports must be through an encrypted and secure means. It also appears the DoH is performing some form of ELR through its Public Health Access system, though it's not clear if COVID-19 reports can be submitted that way. Vermont Y (?) Y No standardized COVID-19 reporting form Phone: (802) 863-7240   Fax: (802) 951-4061   ELR: (802) 651-1619 The Vermont Department of Health offers little in regards to COVID-19 reporting requirements, except to say: "Report all suspect cases immediately to the Vermont Department of Health Infectious Disease Epidemiology by calling 802-863-7240 (24/7)." It's not clear if a subsequent report must also be faxed or sent electronically; contact the health department to confirm. ELR is mentioned on the site's disease reporting page. Virginia ? ? Confidential Morbidity Report Contact: Local health department Other than to say "[c]linical diagnosis of COVID-19 is a reportable condition, regardless of whether testing is pursued or not," the Virginia Department of Health offers little in the way of COVID-19-specific reporting requirements. The DoH indicates that if a patient isn't qualified to be tested by the state lab, clinicians should use the online reporting portal. Additionally, the overall reporting requirements for the DoH are convoluted. The state simply indicates: "Those required to report should report all conditions when suspected or confirmed to their local health department." Washington N Y (?) COVID-19 Extended Form Contact: Local health jurisdiction The Washington State Department of Health doesn't appear to have published any information about specific COVID-19 reporting requirements. The DoH is presumably treating "preliminary or confirmed" COVID-19 cases as an immediately reportable event that "requires a phone call to reach a live person at the [local health jurisdiction], 24/7." It's not clear if a faxed report is also required. The DoH disease reporting web page makes no mention of ELR. West Virginia N (?) Y 2019 Novel Coronavirus (COVID-19) Case Report Form Contact: Local health departments "Report suspect or confirmed cases WITHIN 24 HOURS to the local health department by phone and follow up with written report." It's not clear if ELR is an acceptable form of reporting COVID-19 cases. Wisconsin Y Y Acute and Communicable Disease Case Report F-44151 Contact: Local health department   WEDSS: DHSWEDSS@wisconsin.gov "The state epidemiologist has declared COVID-19 a Category I reportable disease per a memo issued on Feb. 4, 2020. Report immediately by telephone to the patient's local public health department upon identification of a confirmed or suspected case. The local health department shall then notify the state epidemiologist immediately of any confirmed or suspected cases. Within 24 hours, submit a case report electronically through the Wisconsin Electronic Disease Surveillance System (WEDSS), by mail or fax using an Acute and Communicable Disease case report, F44151 or by other means." Wyoming N Y Confidential Disease Report form Phone: 1-888-996-9104   Fax: (307) 777-5573 "Providers and laboratories must report positive [SARS-CoV-2] laboratory tests from commercial reference laboratories to WDH by faxing copies of the laboratory report form to 307-777-5573." According to Wyoming's Reportable Diseases and Conditions List, this faxed report would be in addition to immediate notification by phone. Additionally, "[h]ospital and reference labs with ELR capacity must report positive and negative results," as well as viral detection and serology results. According to that document, COVID-19 isn't a disease preferred for ELR.

Table 2. U.S. territory-based COVID-19 reporting requirements Territory Electronic file (Y/N) Fax? (Y/N) Forms for reporting Contact Additional details American Samoa N N (?) Can't locate the AMS COVID-19 Investigation Form Contact: Facebook page   Phone: (684) 633-5871 or (684) 633-5872 According to American Samoa's report Territory of American Samoa's Response and Action Plan to Combat the Cornoavirus Pandemic, resources for testing are unfortunately thin. It makes mention that the American Samoa Department of Health should be notified "immediately of probable or confirmed cases of COVID-19." It also mentions completing an "AMS COVID-19 Investigation Form." "If there is more than one case of novel coronavirus in a household, local area or facility, or an outbreak is suspects, notify Command Post immediately at (684) 633-5871 or (684) 633-5872." Guam N Y (?) No standardized COVID-19 reporting form Contact: Office of Epidemiology and Research - Phone: (671) 735-7289, Fax: (671) 734-2066 It's clear that Guam is having laboratories report cases of COVID-19, but no reporting requirements for COVID-19 (or any other diseases) can be located on the Department of Public Health and Social Services website. Perhaps contact the Office of Epidemiology and Research for more information. Northern Mariana Islands N N No standardized COVID-19 reporting form Contact: CHCC laboratory The CNMI Department of Public Health has indicated that laboratory testing has been primarily been performed by the Guam Public Health Laboratory, but due to them not being able to meet demand, the CNMI DPH will ship samples to Diagnostic Laboratory Services in Honolulu, Hawaii. Presumably those labs are responsible, in part, for reporting results back to the CNMI. Puerto Rico Unknown Unknown Unknown Phone: (787) 765-2929   Email: contactus@salud.pr.gov The Departamento de Salud de Puerto Rico appears to have had a relevant document OA 440 Sobre la distribución, manejo, administración y reporte de los resultados de las pruebas de COVID-19 concerning reporting results, but the website is down as of April 24, 2020. U.S. Virgin Islands N Y Notification of Infectious Disease Form Phone: St. Croix - (340) 712-6299; St. Thomas and St. John - (340) 776-1519   Fax: Confirm these fax numbers "To report a suspect COVID-19 case, call 3407126299 (STX) or 3407761519 (STT/STJ)." No other COVID-19-specific guidance can be found. The DoH is presumably treating COVID-19 cases as immediately reportable events that should be phoned in. It's possible a follow-up infectious disease form should also be faxed within 24 hours. However, it's not clear if the fax number on the report form is accurate; confirm the fax number during the initial phone call.

3.3 Additional benefits and challenges of laboratory informatics in disease testing and public health

COVID-19 is at the forefront of the consciousness of humanity, by and large, and the informatics tools we implement for managing, treating, and surveilling the disease are of great import. From disease databases to electronic health records, from bioinformatics tools for peptide and protein modeling to laboratory tools such as laboratory information management systems (LIMS) and laboratory information systems (LIS), we continue to fight back against the threat of the SARS-CoV-2 virus. Yet despite the gravity of the pandemic, this is neither the first nor the last time laboratory and scientific informatics will play a positive role in testing for disease and improving public health outcomes.

Health informatics technology, when used responsibly, has already proven to be useful in studying and treating contagious diseases. In a 2013 research paper published in the journal BMJ Quality & Safety, El-Kareh et al. analyzed and described the state of diagnostic health information technology (HIT). They noted that without the aid of HIT, clinicians are more error-prone, leaving them "vulnerable to fallible human memory, variable disease presentation, clinical processes plagued by communication lapses, and a series of well-documented ‘heuristics,’ biases, and disease-specific pitfalls." Appropriate, well-designed HIT systems are capable of helping clinicians and laboratorians by providing more timely access to information, improved communication, better clinical reasoning and decision making, and improved workflows, as well as a reduction in diagnostic errors, and, as a result, improved patient safety and health outcomes.

From a public health perspective, the application of informatics to disease surveillance, reporting, and health habit promotion is also vital. Winters-Miner et al. note in particular the value of using informatics tools and methods to implement predictive analytics and data mining into public health. They use disease prevention and biosurveillance as major examples. We could, for example "analyze large populations of people to quantify risks related to public health, and help physicians to develop intervention programs for those patients at highest risk of some ailment or medical condition." Additionally, through the use of syndromic surveillance systems (tools aiding in the detection of indicators leading up to disease diagnosis for individuals and populations), they suggest that outbreaks can be better detected at local and national levels, and public health measures can be better implemented, increasing public awareness and hindering the spread of disease.

In the clinical laboratory, informatics systems have been influencing workflow improvements and improved service delivery in the lab for more than five decades. And while improvements have been seen in the laboratory from not only the introduction of computerized systems but also the realization of quality control and point-of-care testing, more challenges remain. For example, quality management in the laboratory is still often a manual, time-consuming activity. While the LIS and LIMS have some tools to assist with this task, the inclusion of laboratory analytics and business intelligence tools into those systems may lead to even further quality and efficiencies in the lab. And in the realm of point-of-care testing, oversight and control of instruments can be lost when connectivity and training is lacking. Proper interfacing of these lab instruments could lead to improvements in those areas, says Siemens Healthineers' Daniel Gundler. "Maintaining POC instruments and overseeing the operators performing POC tests would be much easier if all the information and data from each instrument were accessible through one user interface in which coordinators could manage both the instruments and operators."

3.3.1 System interoperability

System interoperability also poses benefits and challenges to clinical disease testing and prevention. Interoperability is defined as “the ability of different information systems, devices and applications (‘systems’) to access, exchange, integrate and cooperatively use data in a coordinated manner” to ensure timely, portable information and improved health outcomes. Improving interoperability among clinical informatics systems is recognized as an important step towards improving health outcomes. The National Academies of Sciences, Engineering, and Medicine had much to say on this topic in their 2015 publication Improving Diagnosis in Health Care:

Improved interoperability across different health care organizations—as well as across laboratory and radiology information systems—is critical to improving the diagnostic process. Challenges to interoperability include the inconsistent and slow adoption of standards, particularly among organizations that are not subject to EHR certification programs, as well as a lack of incentives, including a business model that generates revenue for health IT vendors via fees associated with transmitting and receiving data.

In particular, they discuss an additional concern, one that still causes issues today: interfaces between electronic health records (EHR) and the laboratory and other clinical information systems that feed medical diagnostic information into the EHRs:

Additionally, the interface between EHRs and laboratory and radiology information systems typically has limited clinical information, and the lack of sufficiently detailed information makes it difficult for a pathologist or radiologist to determine the proper context for interpreting findings or to decide whether diagnostic testing is appropriate. For example, one study found that important non-oncological conditions (such as Crohn’s disease, human immunodeficiency virus, and diabetes) were not mentioned in 59 percent of radiology orders and the presence of cancer was not mentioned in 8 percent of orders, demonstrating that the complete patient context is not getting received. Insufficient clinical information can be problematic as radiologists and pathologists often use this information to inform their interpretations of diagnostic testing results and suggestions for next steps. In addition, the Centers for Disease Control and Prevention’s Clinical Laboratory Improvement Advisory Committee (CLIAC) expressed concern over the patient safety risks regarding the interoperability of laboratory data and display discrepancies in EHRs. They recommended that laboratory health care professionals collaborate with other stakeholders to “develop effective solutions to reduce identified patient safety risks in and improve the safety of EHR systems” regarding laboratory data.

In fact, interoperability issues have come up during the global laboratory response to the COVID-19 pandemic. In early April 2020, a report from Nature revealed that academic research laboratories wanting to assist with COVID-19 testing efforts have at times been stymied by the incompatibility between academic informatics systems and hospital EHRs. Not only do hospitals use EHRs of differing types, but many of those EHRs were not designed to talk to other EHRs, let alone to academic and research laboratories' informatics systems. Combine this with strict account procedures and the costs of developing interfaces on-the-fly, more than a few medical systems have turned away the offer of help from academic and research labs. As it turns out, HL7- other standard-based interfaces have long been expensive for many vendors to implement, the cost justified typically when high volumes of samples are involved. Additionally, in more normal, non-pandemic circumstances, the requirement to interface with EHRs and hospital information systems (HIS) is almost exclusively found in the LIS and LIMS used in patient settings, i.e., in the hospitals, medical offices, and laboratories catering to diagnosing disease in patients. Academic labs have not been equipped at any level (software, hardware, or personnel) to do high volume clinical testing, nor have they had reason to ensure their informatics systems can interface with clinical systems.

Interoperability benefits and challenges show up elsewhere too. Take for example the value of phenotypes, a representation of the genetic analysis of the collective observable traits of an organism, traits caused by the interaction of its genome with the environment. The value of patient phenotyping data is increasingly useful in the fight against known and novel viruses, as well as a broad variety of non-viral diseases. As Ausiello and Shaw note, in order for medicine to advance and produce improved patient outcomes, "traditional clinical information must be combined with genetic data and non-traditional phenotypes and analyzed in a manner that yields actionable insights into disease diagnosis, prevention, or treatment." Whether it's identifying "the measurable phenotypic characteristics of patients that are most predictive of individual variation" in treatment outcomes for chronic pain or COVID-19, phenotypes have utility in the clinical sector.

Here again interoperability between EHRs and laboratory informatics systems comes into play. In a 2019 paper published by Zhang et al. in nph Digital Medicine, the topic of extracting patient phenotypes from laboratory test results fed into EHRs is addressed. The authors state that one of the more difficult aspects of their research is that while "[l]aboratory tests have broad applicability for translational research ... EHR-based research using laboratory data have been challenging because of their diversity and the lack of standardization of reporting laboratory test results." They add:

Despite the great potential of EHR data, patient phenotyping from EHRs is still challenging because the phenotype information is distributed in many EHR locations (laboratories, notes, problem lists, imaging data, etc.) and since EHRs have vastly different structures across sites. This lack of integration represents a substantial barrier to widespread use of EHR data in translational research.

The answer to the clinical and laboratory interoperability question is unclear. A 2019 article in the American Association for Clinical Chemistry's CLN Stat addressed remaining roadblocks, including lack of standards development, data quality issues, clinical data matching, lack of incentivizing health IT optimization, text-based reporting formats, differences in terminology, and HL7 messaging issues. They add that proposals from the Office of the National Coordinator for Health Information Technology (ONC) and the Centers for Medicare and Medicaid Services include possible fixes such as standardized application programming interfaces (API). They also note that middleware may pick up the slack in connecting more laboratory devices, rather than depending on the LIS to handle all the interfacing.

Even so, it remains obvious that more work needs to be done in the development and standard use of clinical and laboratory informatics applications if the promise of personalized medicine and the need for improved disease testing and response are to be fulfilled. In particular, how we responsibly protect personal health information while putting its anonymized variants to beneficial use for disease testing and prevention remains a critical question that must be solved in order to better prepare for the next COVID-19.