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

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 activites 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 obsevational 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 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 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 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.

Somewhat related are any internal reporting requirements, particularly for test reporting in labs and medical facilities. The International Statistical Classification of Diseases and Related Health Problems (ICD) is a 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. Green and Bradley provide insight into these additions, as does the American Academy of Pediatrics.

Laboratories analyzing specimens for SARS-CoV-2 therefore must be equipped to not only handle analytical testing and test orders using the new test codes, but they also must be able to quickly and accurately transfer vital case information to the appropriate health authority.

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 California 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. The also offers 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. 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 facilitites, 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 immeadiately 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 medicall 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

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

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 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.

https://www.nature.com/articles/s41746-019-0110-4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4204239/ https://www.nap.edu/read/21794/chapter/7#241 https://www.mlo-online.com/home/article/13017228/poct-made-easier-with-informatics