Using Environmental Surveillance to Detect Vaccine-Preventable Diseases in Northern Ghana Restricted; Files Only

Abstract

Environmental Surveillance (ES) has been increasingly used for COVID-19 surveillance and can also be expanded to other pathogens. Currently, there is limited surveillance of SARS-CoV-2 in Northern Ghana where no clinical cases have been reported since the beginning of the pandemic in March 2020. We applied ES in a rural area, not only for SARS-CoV-2 but also for three other diseases, and used schools as the sampling site. Samples were collected from latrines and septic tanks in nine schools and one residential teaching college in Nanumba North District and nine schools in Mion District. Real-time quantitative polymerase chain reaction (PCR) was used to detect four target pathogens (SARS-CoV-2, Rotavirus, Salmonella Typhi, and Vibrio cholera) from a total of 114 environmental samples.

Results showed that SARS-CoV-2 (22% POS) and Vibrio cholera (6% POS) were the most frequently detected pathogens in the environmental samples from schools and the college. The samples from college residential halls had a higher proportion of PCR-positive tests (43.3%) compared to samples from Primary and Junior High Schools (26.2%). This is a novel and significant finding in a rural setting in Ghana that demonstrates the feasibility and value of ES for infectious disease surveillance in remote areas. We conclude that it would be helpful to expand the implementation of ES to other rural areas of Ghana and other low- and middle-income settings and use the results to better target vaccination campaigns and other prevention and control measures.

Table of Contents

Literature Review 1

Environmental Surveillance 1

Environmental Surveillance for Polio in Ghana 2

Environmental Surveillance across Africa 3

SARS-CoV-2 4

Vibrio cholera 6

Rotavirus 7

Salmonella Typhi 8

Introduction 9

Infectious Disease Surveillance 9

Environmental Surveillance 10

Research Questions 12

Objectives 12

Study Sites 14

Methods 17

Laboratory analysis 17

PCR Protocols 18

Study Location 1: Nanumba North District 19

Study Location 2: Mion District 21

Data analysis 27

Results 27

Study Location 1. Nanumba North District 27

Study Location 2. Mion District 32

Discussion 40

Study Location #1: Nanumba North District 40

Study Location #2: Mion District 42

Limitations 44

Conclusions 47

References 48

LIST OF TABLES

Table 1. Triplex Real-time PCR Primer and Probe Sequence for each target organism 19

Table 2. Nanumba North District School Sampling Sites 20

Table 3. Sample collection sites in Bimbila and Chamba 21

Table 4. Mion District School Sampling Site Population Figures 22

Table 5. Sample collection sites in Sambu and Sang. 22

Table 6. Detection of target pathogens in environmental samples (n=27) from Bimbila Cluster 1& Cluster 2 Basic Schools and the Bimbila Senior High School, September 27^th to October 20^th, 2022. 29

Table 7. Detection of target pathogens in environmental samples from Female and Male Residential Halls at the E.P College of Education (n=25) in Bimbila, September 27^th to October 20^th, 2022. 30

Table 8. Detection of target pathogens in environmental samples (n=16) from Chamba Cluster 1 Basic Schools, September 27^th to October 20^th, 2022. 31

Table 9. Detection of target pathogens in environmental samples (n=22) from Islamic Primary and Junior School and Sambu Model Junior High School, October 25^th to November 18^th,2022. 35

Table 10. Detection of target pathogens in environmental samples from Sang Primary, Junior School and Senior High School (n=24) in Sang, September 27^th to October 20^th, 2022. 36

Table 11. Detection of target pathogens in environmental samples from Bimbila, Chamba, Sambu, and Sang (n=114), September 27^th to November 18^th, 2022 38

LIST OF FIGURES

Figure 1. The Northern Region 14

Figure 2. Nanumba North District Municipality 15

Figure 3. Mion District Assembly 16

Figure 4. Bimbila Sample Points in Nanumba North District 23

Figure 5. Chamba Sample Points in Nanumba North District 24

Figure 6. Sambu Sample Points in Mion District 25

Figure 7. Sang Sample Points in Mion District 26

Figure 8. Percent of environmental samples that were positive for each target organism 28

Figure 9. Distribution of Ct values for four pathogen targets in 68 environmental samples from ten schools in Bimbila and Chamba 32

Figure 10. Percent of environmental samples that were positive for each target organism 33

Figure 11. Distribution of Ct values for four pathogen targets in 46 environmental samples from nine schools in Sambu and Sang 34

Figure 12. Distribution of Ct values for all target organisms from Nanumba North and Mion District in 114 environmental samples 37

Figure 13. Detection of SARS-CoV-2 in Female Residential Halls at the E.P College of Education in Bimbila 38

Figure 14. Detection of SARS-CoV-2 in Male Residential Halls at the E.P College of Education in Bimbila 39

Figure 15. Proportion (%) of persons fully vaccinated by Region and District 45

Figure 16. Active COVID-19 cases in Ghana by region, March 31st, 2023. 46

About this Master's Thesis

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School	Rollins School of Public Health
Department	Hubert Department of Global Health
Degree	M.P.H.
Submission	Master's Thesis
Language	English
Research Field	Environmental Sciences Health Sciences, Public Health
Palavra-chave	Wastewater Environmental Surveillance Infectious Disease SARS-CoV-2
Committee Chair / Thesis Advisor	Christine L. Moe, Ph.D., Emory University

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