Difference between revisions of "LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory"

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(Updated for July 1.1 update)
(Updated for Edition 2.0)
 
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'''Title''': ''COVID-19 Testing, Reporting, and Information Management in the Laboratory''
 
'''Title''': ''COVID-19 Testing, Reporting, and Information Management in the Laboratory''
  
'''Edition''': Edition 1.1
+
'''Edition''': Edition 2.0
  
 
'''Author for citation''': Shawn E. Douglas
 
'''Author for citation''': Shawn E. Douglas
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'''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]
 
'''License for content''': [https://creativecommons.org/licenses/by-sa/4.0/ Creative Commons Attribution-ShareAlike 4.0 International]
  
'''Publication date''': July 2020
+
'''Publication date''': August 2020
  
  
 
This guide discusses the evolving status of [[laboratory]] testing, reporting, and [[information management]] for the [[COVID-19]] disease and pandemic. The focus is primarily on testing and reporting in the United States, but other parts of the world are also addressed. It also examines the disease's history, what makes it difficult to combat, and what diagnostic testing methods are currently available. Additionally, the guide examines what testing workflow for COVID-19 is like, along with the equipment, software, and reporting required by testing labs, as well as additional benefits and challenges of [[laboratory informatics]] in disease testing and public health. This guide closes with final remarks, as well as a listing of associated resources, including guidance documents, web portals, and key reading.  
 
This guide discusses the evolving status of [[laboratory]] testing, reporting, and [[information management]] for the [[COVID-19]] disease and pandemic. The focus is primarily on testing and reporting in the United States, but other parts of the world are also addressed. It also examines the disease's history, what makes it difficult to combat, and what diagnostic testing methods are currently available. Additionally, the guide examines what testing workflow for COVID-19 is like, along with the equipment, software, and reporting required by testing labs, as well as additional benefits and challenges of [[laboratory informatics]] in disease testing and public health. This guide closes with final remarks, as well as a listing of associated resources, including guidance documents, web portals, and key reading.  
  
This first edition is published in a time when information about COVID-19 and the SARS-CoV-2 virus is still changing rapidly. An attempt to make small, incremental updates to the guide will be made as the state of reasearch and testing continues to shift.
+
This guide is published in a time when information about COVID-19 and the SARS-CoV-2 virus is still changing rapidly. An attempt to make small, incremental updates to the guide will be made as the state of reasearch and testing continues to shift. The occasional major update will increment the edition a full number. August's 2.0 edition brings with it a new Chapter 3 (bumping the prior Chapter 3 and 4 back) focusing on how a laboratory can get set up with COVID-19 and other respiratory virus testing.
  
 
The table of contents for ''COVID-19 Testing, Reporting, and Information Management in the Laboratory'' is as follows:  
 
The table of contents for ''COVID-19 Testing, Reporting, and Information Management in the Laboratory'' is as follows:  
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::2.4.1 Background on the laboratory testing environment
 
::2.4.1 Background on the laboratory testing environment
 
::2.4.2 PCR-based
 
::2.4.2 PCR-based
::2.4.3 LFA- and LAMP-based
+
::2.4.3 LFA and isothermal amplification methods
 
::2.4.4 Blood serum
 
::2.4.4 Blood serum
::2.4.5 Testing alternatives and challenges
+
::2.4.5 Antigen tests
 +
::2.4.6 Testing alternatives and challenges
  
3. [[LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Workflow and information management for COVID-19 (and other respiratory diseases)|Workflow and information management for COVID-19 (and other respiratory diseases)]]
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3. [[LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Adding COVID-19 and other virus testing to your laboratory|Adding COVID-19 and other virus testing to your laboratory]]
  
:3.1 Laboratory informatics and workflow management
+
:3.1 What methodologies will you use?
::3.1.1 Does the system provide a flexible provider portal?
+
::3.1.1 PCR
::3.1.2 Does the system allow for the flexible addition of users, providers, and patients?
+
::3.1.2 Pooled testing
::3.1.3 Does the system allow for laboratory workflows sympathetic to COVID-19 and other types of respiratory illness testing?
+
::3.1.3 Rapid antigen testing
::3.1.4 Does the system allow for interfacing with most instruments currently used for testing for COVID-19?
+
::3.1.4 LAMP and CRISPR
::3.1.5 Does the system allow for versatile viewing and reporting of COVID-19 results?
+
::3.1.5 Point-of-care and other alternative testing
:3.2 Laboratory informatics and reporting requirements
+
:3.2 What kind of space, equipment, and supplies will you need?
::3.2.1 ICD and CPT coding
+
::3.2.1 Laboratory space arrangements
::3.2.2 Reporting to local and regional health departments
+
::3.2.2 Instruments and assays
:3.3 Additional benefits and challenges of informatics in disease testing and public health
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::3.2.3 Reagents
::3.3.1 System interoperability
+
::3.2.4 Consumables
::3.3.2 Contact tracing
+
::3.2.5 Software and services
 +
::3.2.6 Major vendors and consultants
 +
:3.3 What other considerations should be made?
 +
::3.3.1 U.S. regulatory compliance
 +
::3.3.2 Reporting
 +
::3.3.3 Billing, Medicare, and Medicaid
  
4. [[LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Final thoughts and additional resources|Final thoughts and additional resources]]
+
4. [[LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Workflow and information management for COVID-19 (and other respiratory diseases)|Workflow and information management for COVID-19 (and other respiratory diseases)]]
  
:4.1 Final thoughts
+
:4.1 Laboratory informatics and workflow management
:4.2 Key guidance documents
+
::4.1.1 Does the system provide a flexible provider portal?
:4.3 Web portals
+
::4.1.2 Does the system allow for the flexible addition of users, providers, and patients?
:4.4 Key journal articles
+
::4.1.3 Does the system allow for laboratory workflows sympathetic to COVID-19 and other types of respiratory illness testing?
:4.5 Public health lab directory
+
::4.1.4 Does the system allow for interfacing with most instruments currently used for testing for COVID-19?
:4.6 Test kit and other resources
+
::4.1.5 Does the system allow for versatile viewing and reporting of COVID-19 results?
:4.7 Public health laboratory informatics vendors
+
:4.2 Laboratory informatics and reporting requirements
 +
::4.2.1 ICD, CPT, and HCPCS coding
 +
::4.2.2 Reporting to local and regional health departments
 +
:4.3 Additional benefits and challenges of informatics in disease testing and public health
 +
::4.3.1 System interoperability
 +
::4.3.2 Contact tracing
 +
 
 +
5. [[LII:COVID-19 Testing, Reporting, and Information Management in the Laboratory/Final thoughts and additional resources|Final thoughts and additional resources]]
 +
 
 +
:5.1 Final thoughts
 +
:5.2 Key guidance documents
 +
:5.3 Web portals
 +
:5.4 Key journal articles
 +
:5.5 Public health lab directory
 +
:5.6 Test kit and other resources
 +
:5.7 Public health laboratory informatics vendors
  
 
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<!---Place all category tags here-->

Latest revision as of 19:18, 23 August 2020

SARS-CoV-2 without background.png

Title: COVID-19 Testing, Reporting, and Information Management in the Laboratory

Edition: Edition 2.0

Author for citation: Shawn E. Douglas

License for content: Creative Commons Attribution-ShareAlike 4.0 International

Publication date: August 2020


This guide discusses the evolving status of laboratory testing, reporting, and information management for the COVID-19 disease and pandemic. The focus is primarily on testing and reporting in the United States, but other parts of the world are also addressed. It also examines the disease's history, what makes it difficult to combat, and what diagnostic testing methods are currently available. Additionally, the guide examines what testing workflow for COVID-19 is like, along with the equipment, software, and reporting required by testing labs, as well as additional benefits and challenges of laboratory informatics in disease testing and public health. This guide closes with final remarks, as well as a listing of associated resources, including guidance documents, web portals, and key reading.

This guide is published in a time when information about COVID-19 and the SARS-CoV-2 virus is still changing rapidly. An attempt to make small, incremental updates to the guide will be made as the state of reasearch and testing continues to shift. The occasional major update will increment the edition a full number. August's 2.0 edition brings with it a new Chapter 3 (bumping the prior Chapter 3 and 4 back) focusing on how a laboratory can get set up with COVID-19 and other respiratory virus testing.

The table of contents for COVID-19 Testing, Reporting, and Information Management in the Laboratory is as follows:


1. Overview of COVID-19 and its challenges

1.1 COVID-19: The terminology
1.2 COVID-19: History and impact (so far)
1.3 Challenges of managing the disease in the human population

2. Diagnostic testing of COVID-19 and other coronaviruses

2.1 Testing terminology
2.1.1 Introduction
2.1.2 Polymerase chain reaction (PCR)
2.1.3 Lateral flow assay (LFA)
2.2 Testing conducted on previous coronaviruses
2.2.1 Severe acute respiratory syndrome (SARS)
2.2.2 Middle East respiratory syndrome (MERS)
2.2.3 The common cold
2.3 Organizational and agency guidance on COVID-19 testing
2.3.1 Regulatory considerations: HIPAA and CLIA
2.4 Current test methods and their differences
2.4.1 Background on the laboratory testing environment
2.4.2 PCR-based
2.4.3 LFA and isothermal amplification methods
2.4.4 Blood serum
2.4.5 Antigen tests
2.4.6 Testing alternatives and challenges

3. Adding COVID-19 and other virus testing to your laboratory

3.1 What methodologies will you use?
3.1.1 PCR
3.1.2 Pooled testing
3.1.3 Rapid antigen testing
3.1.4 LAMP and CRISPR
3.1.5 Point-of-care and other alternative testing
3.2 What kind of space, equipment, and supplies will you need?
3.2.1 Laboratory space arrangements
3.2.2 Instruments and assays
3.2.3 Reagents
3.2.4 Consumables
3.2.5 Software and services
3.2.6 Major vendors and consultants
3.3 What other considerations should be made?
3.3.1 U.S. regulatory compliance
3.3.2 Reporting
3.3.3 Billing, Medicare, and Medicaid

4. Workflow and information management for COVID-19 (and other respiratory diseases)

4.1 Laboratory informatics and workflow management
4.1.1 Does the system provide a flexible provider portal?
4.1.2 Does the system allow for the flexible addition of users, providers, and patients?
4.1.3 Does the system allow for laboratory workflows sympathetic to COVID-19 and other types of respiratory illness testing?
4.1.4 Does the system allow for interfacing with most instruments currently used for testing for COVID-19?
4.1.5 Does the system allow for versatile viewing and reporting of COVID-19 results?
4.2 Laboratory informatics and reporting requirements
4.2.1 ICD, CPT, and HCPCS coding
4.2.2 Reporting to local and regional health departments
4.3 Additional benefits and challenges of informatics in disease testing and public health
4.3.1 System interoperability
4.3.2 Contact tracing

5. Final thoughts and additional resources

5.1 Final thoughts
5.2 Key guidance documents
5.3 Web portals
5.4 Key journal articles
5.5 Public health lab directory
5.6 Test kit and other resources
5.7 Public health laboratory informatics vendors