Longitudinal SARS-CoV-2 Fecal Shedding in COVID-19 Patients Open Access

Fenin, Kimberly (Spring 2023)

Permanent URL: https://etd.library.emory.edu/concern/etds/m900nv868?locale=en



The COVID-19 pandemic (Coronavirus disease 2019), which is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has been a global emergency since its emergence in 2019. Although most individuals infected with COVID-19 have mild symptoms, a subset of people develop severe illness.


The aim of this study is to evaluate infection in patients diagnosed with COVID-19 by assessing the magnitude and duration of viral SARS-CoV-2 shedding in fecal samples.


52 patients were admitted to Emory University Hospital and diagnosed with COVID-19. In addition, clinical symptoms were collected. A total of 162 fecal samples were collected from these patients between days 1 and 42. Digital PCR was used to determine the concentrations of SARS-CoV-2, PMMoV (Pepper mild mottle virus), mtDNA (mitochondrial DNA), and BRSV (Bovine respiratory syncytial virus) in the 162 fecal samples. The clinical and laboratory data were combined into a single database, and inferential statistical analysis was conducted to investigate the relationships between patients, their clinical data, and the results obtained from the analysis of the fecal samples.


The combined dataset had a total of 52 patients and 162 fecal samples that were run through Digital PCR for concentrations of SARS-CoV-2, PMMoV, mtDNA and BRSV. The data showed that out of 162 samples, 37 tested positive for SARS-CoV-2 using digital PCR. Among 37 positive samples, 13 patients (35%) had a low concentration (~4.8×103) of virus load, 15 (41%) had medium viral shedding (~9.0×105 ) on all days tested. 5 (13%), had a high concentration (~5.7×108) of viral load at the beginning of the study on days 1,3, and 7. Negative results indicated that no viral shedding was present from days 14-42. There was also no significant association observed between mtDNA, SARS-CoV-2 and PMMoV titers.


Understanding the duration and magnitude of SARS-CoV-2 fecal shedding in COVID-19 patients is critical for comprehending the disease and developing treatment strategies. This is because both illness severity and viral shedding are crucial outcomes that determine the spread of the infection.

Table of Contents

Chapter I: Introduction and Literature review Review1

1.    Introduction2

2.    Virus/Genome Organization4

3.    COVID-19 Diagnosis9

4.    Clinical Symptoms and incubation period15

5.    Transmission17

6.    Prevention and Control18

7.    Vaccine Development28

Chapter II: Materials and Methods26

1.    Material and Methods26

2.    Stool Collection26

3.    Fecal Sample Processing and Nucleic Acid Extraction27

4.    COVID-19 Symptoms and Scoring28

5.    Quantification of SARS-CoV-2, PMMoV, and mtDNA in Stool Samples using dPCR28

6.    Statistical Analysis30

7.    Results30

8.    Discussion33

9.    Tables38

10. References49


Chapter III: Conclusions /Limitations / Public Health


1.    Conclusions56

2.    Limitations56

3.  Public Health Significances56

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