Occurrence and Magnitude of Norovirus Contamination and Quantitative Microbial Risk Assessment (QMRA) of Norovirus in Accra, Ghana 公开

Tsai, Han-Hsuan (2014)

Permanent URL: https://etd.library.emory.edu/concern/etds/np193968d?locale=zh
Published

Abstract

Noroviruses (NoVs) are the major cause of nonbacterial gastroenteritis worldwide. NoV genogroup I (GI) and genogroup II (GII) are the most predominant strains that cause disease among humans. NoVs are primarily transmitted via the fecal-oral route and through contaminated environments. However, research on NoV exposure pathways, contamination levels, and the corresponding risk of NoV infection is limited, particularly in low income urban settings.

In this study, environmental samples were collected from a variety of domains in Accra, Ghana, in order to investigate NoV GI and GII levels in the environment. Samples were screened for the presence of NoV GI and/or GII, and the samples that contained PCR inhibitors or were NoV positive in the screening step were further quantified. The results of the environmental investigation showed that a high percentage (41% for NoV GI and 52% for NoV GII) of septage samples collected from public latrines were NoV-positive. In addition, 5% to 15% of samples collected from public drains, flooded areas, irrigation systems, and farms were also NoV-positive. The NoV GI and GII concentrations in irrigation and farm water samples were used to conduct Quantitative Microbial Risk Assessment (QMRA) to investigate the potential risk of NoV infection among farmers who unintentionally ingest NoV contaminated water while working. The QMRA results showed that, for farmers who work for seven days in the field, the estimated average probabilities of NoV GI and GII infection are 0.28 and 0.42, respectively,

The PCR inhibition for NoVs and Adenovirus and the sensitivity analysis of the decision making scheme used to determine whether the samples were positive were also analyzed. The results of sensitivity analysis showed that the changes in frequencies of positive, negative, inhibition positive, and inhibition negative samples were significant if the decision scheme became stricter; however, the changes in average concentrations among different schemes were not significant. The results of PCR inhibition showed that there 18%, 19%, and 2% of samples inhibited for NoV GI, NoV GII, and Adenovirus, respectively, and 18 out of 25 (72%) of samples that were inhibited for Adenovirus were also inhibited for NoVs.

Table of Contents

Table of Contents

Chapter 1: Literature Review.. 1

NOROVIRUS EPIDEMIOLOGY.. 1

GENOTYPE, STRUCTURE AND DETECTION OF NOROVIRUS. 4

TRANSMISSION OF NOROVIRUS. 7

PREVALENCE OF NOVS IN ENVIRONMENTAL AND FOOD SAMPLES. 9

QUANTITATIVE MICROBIAL RISK ASSESSMENT. 12

Introduction of Quantitative Microbial Risk Assessment 12

Using QMRA to estimate NoV related health adverse outcomes. 14

Using QMRA to estimate the health outcomes in urban settings. 16

EPIDEMIOLOGICAL AND ENVIRONMENTAL NOV RESEARCH IN GHANA 17

FUTURE RESEARCH.. 19

REFERENCES. 21

Chapter 2: Viral Testing and Quantitative Microbial Risk Assessment 31

ABSTRACT. 31

INTRODUCTION.. 31

METHODS. 34

Sample collection and pretreatment 34

RNA extraction and detection. 39

Data analysis. 41

QMRA method. 42

RESULTS. 45

Number and concentrations of positive samples from different domains. 45

DISCUSSION.. 49

REFERENCES. 53

FIGURES. 58

Figure 1. The decision scheme of determining whether the sample was positive and/or quantifiable 58

Figure 2. The distribution of log NoV GI concentration (left) and log NoV GII concentration (right) 59

Figure 3. Estimated seven-day probability of NoV GI infection among farmers who unintentionally ingest contaminated water 60

Figure 4. Estimated seven-day probability of NoV GII infection among farmers who unintentionally ingest contaminated water 61

TABLES. 62

Table 1. NoV detection results for food samples collected from markets and street vendors 62

Table 2. NoV detection results for samples collected from households. 62

Table 3. NoV detection results for samples collected from public latrines. 63

Table 4. NoV detection results for samples collected from schools. 63

Table 5. NoV detection results for samples collected from oceans and beaches 64

Table 6. NoV detection results for samples collected from public domains, flood, or public drains 64

Table 7. NoV detection results for samples collected from nurseries. 65

Table 8. NoV detection results for samples collected from farms and irrigation water 65

Table 9. Summary of NoV GI concentrations. 66

Table 10. Summary of NoV GII concentrations. 66

APPENDIX.. 68

R codes for QMRA.. 68

Chapter 3: Sensitivity Analysis of the real-time PCR Decision Scheme and Inhibition Analysis 71

SENSITIVITY ANALYSIS OF THE DECISION SCHEME.. 71

Methods of analyzing modified decision schemes. 71

Results of modifying the decision scheme. 72

INHIBITION ANALYSIS. 74

Results of inhibition analysis. 75

RECOMMENDATIONS FOR FUTURE RESEARCH.. 77

REFERENCES. 79

FIGURE.. 81

Figure 5. The original decision scheme, the modified scheme A, and the modified scheme B 81

TABLES. 82

Table 11. Frequency of NoV GI positive results using the three decision schemes 82

Table 12. Frequency of NoV GII positive results using the three decision schemes 82

Table 13. Comparison of NoV GI concentrations in septage and particulate samples using the three decision schemes. 83

Table 14. Comparison of NoV GI concentrations in environmental water and swab samples using the three decision schemes. 83

Table 15. Comparison of NoV GII concentrations of septage and swab samples using the three decision schemes. 84

Table 16. Comparison of NoV GII concentrations of particulate samples collected from households and public domain using the three decision schemes. 84

Table 17. Comparison of NoV GII concentrations of particulate samples collected from public drain, flooding areas, and farms using the three decision schemes. 86

Table 18. Comparison of NoV GII concentrations of environmental water samples using the three decision schemes. 86

Table 19. Frequency of target detection and inhibition with QuantiFast Pathogen + IC Assay 87

Table 20. Co-occurrence of inhibition across assays and sample types. 87

Chapter 4: Public Health Implications and Future Research. 87

PUBLIC HEALTH IMPLICATIONS. 87

FUTURE RESEARCH.. 88

REFERENCES. 91

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