Surveillance for COVID-19 Using Wastewater and Advancing Nasal Self-Collection of Specimens (SWANSS) in an Atlanta Jail Public

Abstract

Background: Correctional facilities historically house some of the most vulnerable persons in our society. With crowded living conditions, decreased access to quality medical care, and limited resources, infectious disease outbreaks can be extremely dangerous, particularly for highly transmissible diseases like COVID-19. Wastewater-Based Surveillance is a low- cost, highly sensitive, non- invasive method that can provide an early warning of COVID-19 surges in the community and outbreaks in institutions, but this has not yet been applied in correctional facilities.

 

Objective: The study’s main objective was to examine if WBS is a practical and sensitive strategy to surveil for new COVID-19 outbreaks in a large jail setting.

 

Methods: The study period was from June 15, 2021 to March 16, 2022 (39 weeks). COVID-19 diagnostic tests were administered to jail residents and analyzed on a weekly basis—rapid diagnostic test data was collected daily by the jail administration, and 16 mass PCR testing events were conducted by the study team. Wastewater samples were collected via Moore swabs on 28 unique weeks and analyzed for SARS-CoV-2 by realtime RT-qPCR. Temporal and correlation analysis were applied to wastewater and COVID-19 diagnostic test results to examine the association between the prevalence of COVID-19 identified by diagnostic testing and detection of SARS-CoV-2 RNA in the wastewater.

 

Results: The efficiency of diagnostic testing increased with repeated trials and improved staffing. During the study period, COVID-19 test positivity ranged from 0% to 29.5%. SARS-CoV-2 RNA was detected in the wastewater samples from 25 of the 28 weeks with samples. Wastewater collection and analysis was feasible for a team with a designated sampling and lab team. Stronger RT-PCR signals for SARS-CoV-2 in the jail wastewater preceded rises in the number of COVID-19 cases in the jail, and regression analysis indicated a strong relationship between SARS-CoV-2 RNA concentrations in wastewater samples and positivity rates of COVID-19 diagnostic testing.

Conclusions SARS-CoV-2 RNA detection in wastewater collected at the jail was associated with COVID-19 diagnostic test results in the jail population. Wastewater based surveillance is a practical strategy to surveil for new COVID-19 outbreaks in a jail setting.

Table of Contents

Chapter 1:

Introduction_________________________________________________________________________________1

Chapter 2:

Literature Review___________________________________________________________________________ 3

COVID-19 in United States Correctional Facilities_______________________________________3

Infectious Diseases in Correctional Facilities____________________________________________4

COVID-19 in Correctional Facilities______________________________________________________6

COVID-19 Diagnostics Methods__________________________________________________________7

COVID-19 Diagnostics in Jails____________________________________________________________8

Wastewater Based Surveillance for COVID-19 ___________________________________________9

      Overview____________________________________________________________________________9

Wastewater Based Surveillance Methods___________________________________________9

Previous Studies on Wastewater Surveillance ____________________________________12

Fecal Shedding Characteristics____________________________________________________12

Wastewater Surveillance at Institutions___________________________________________13

Wastewater Based Surveillance in a Jail__________________________________________________15

Chapter 3:

Introduction_________________________________________________________________________________16

Research Objective__________________________________________________________________________18

Rationale____________________________________________________________________________________18

Methods_____________________________________________________________________________________19

COVID-19 Diagnostic testing_____________________________________________________________19

           PCR Nasal Swab Collection_________________________________________________________19

_ RT-PCR Test Procedure____________________________________________________________________20

           Rapid Test Collection_______________________________________________________________21

Wastewater Based Surveillance___________________________________________________________22

               Sample Collection__________________________________________________________________22

                Laboratory Analysis________________________________________________________________23

                 Interpreting Results_______________________________________________________________23

Data Analysis______________________________________________________________________________25

           COVID-19 Diagnostic Testing Analysis_____________________________________________25

           Wastewater Data Analysis___________________________________________________________26

Results________________________________________________________________________________________27

COVID-19 Diagnostic Testing_____________________________________________________________28

     Wastewater Testing Results_______________________________________________________________33

Relationship between Diagnostic Test Results and Wastewater Monitoring Results____35

Discussion____________________________________________________________________________________41

     Mass COVID-19 Diagnostic Testing in a Jail______________________________________________41

WBS Testing in a Jail_______________________________________________________________________44

Using WBS to predict individual diagnostic cases________________________________________46

Strengths____________________________________________________________________________________ 48

Limitations__________________________________________________________________________________ 48

Conclusion__________________________________________________________________________________ 50

Chapter 4:

Recommendations__________________________________________________________________________ 51

References___________________________________________________________________________________52

About this Master's Thesis

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• Permission granted by the author to include this thesis or dissertation in this repository. All rights reserved by the author. Please contact the author for information regarding the reproduction and use of this thesis or dissertation.

School	Rollins School of Public Health
Department	Hubert Department of Global Health
Degree	M.P.H.
Submission	Master's Thesis
Language	English
Research Field	Health Sciences, Public Health Health Sciences, Epidemiology
Mot-clé	Diagnostic Testing COVID-19 Jail Wastewater Based Surveillance
Committee Chair / Thesis Advisor	Moe, Christine, Emory University
Committee Members	Spaulding, Anne, Emory University

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