A unique cost-effective disease surveillance model for southern African village pigs and chickens

Abstract

Pig and chicken farming provide an important protein and revenue source for communities in developing countries. Despite these benefits, these two sectors in the Eastern Cape Province (ECP) of South Africa are still underdeveloped and poorly surveyed for pig and chicken diseases. The mechanisms for early detection of diseases remain a challenge, consequently, mortalities due to important infectious diseases are frequent. While the province faces a critical shortage of veterinary resources including limited budget, this tudy aims to examine ways by which animal disease surveillance in the ECP could be better targeted to enable more efficient use of existing veterinary resources. Consequently, the overall objective of this study was to propose a system to promote early detection of pig and chicken diseases, based on social network and value chain analyses, which could be combined using ensemble modelling. Ensemble modelling is the process of running two or more related but different analytical models and then synthesizing the results into a single outcome. The work presented in this thesis was broken down into a hazard analysis component, farming and disease management component, risk analysis component and a proposal on a placement of surveillance units in the trade hubs identified by social network analysis. Each component had its own separate outcome. These components were thereafter combined to create an ensemble model for cost-effective surveillance of the smallholder pig and chicken farming sector in the ECP. Within this context, a hazard analysis was a review of pig and chicken diseases in the province from 2000–2020. This review included relevant published papers identified by a computerized literature search from Web of Science; provincial animal health reports; the national database from the Department of Agriculture, Land Reform and Rural Development (DALRRD); animal health reports submitted by DALRRD to the World Organization for Animal Health (WOAH) via the World Animal Health Information Database (WAHID) interface and laboratory records. The review identified 174 publications of which 26 were relevant based on the selection criteria. Classical swine fever and Newcastle disease were the most reported diseases in pigs and chickens respectively, and they were consistently recorded in both the National database and WOAH database. These diseases were therefore used as the primary hazards in the ensemble model. The retrieved literature on pig and chicken diseases was scarce and no longer up to date, providing decision makers with no current information on which disease to prioritize. The review identified zoonotic diseases that require further studies yet failed to find information on important neglected diseases like leptospirosis. To establish how farmers dealt with chicken diseases, a sociological survey of chicken farmers and the remedies most used to prevent diseases in their flocks was conducted throughout the ECP between February 2019 and June 2019, alongside a serological survey to estimate the apparent seroprevalence of selected chicken diseases in the province (from August 2019 to March 2020). Most chicken farmers in the survey were females and pensioners (69 % and 66.1 % respectively) and had a primary school education (47.1 %). Traditional remedies were commonly used by farmers (47.15 %) and among the remedies, 136 Aloe plant (Aloe ferox Mill.) or “ikhala” in local language (isiXhosa) was the most used product (28.23 %) to prevent and reduce mortalities among village chickens. The second 138 group of remedies used by farmers was antibiotics with tetracyclines being the most used remedy under this category (17.42 %) followed by Sulpha products (12.01 %). The conclusions drawn from this component were: i) the sector was dominated by pensioners with a low level of education; ii) village chickens could be a potential source of emerging diseases including virulent Newcastle disease virus (NDV) because of the lack of vaccination and biosecurity by farmers; iii) the use of antibiotics by untrained chicken farmers was a major public health concern as it could serve as a source of antimicrobial resistance (AMR); iv) the overall seroprevalence of Newcastle disease 146 (ND), avian influenza (AI), avian infectious bronchitis (IB) and Mycoplasma 147 gallisepticum (MG) in the province were 69.2 % (95 % CI 51.9 - 86.5%); 1.8 % (95 % 148 CI 0.2 - 3.4%); 78.5 % (95 % CI 74.9 - 82%) and 55.8 % (95 % CI 41.3 - 70.3%) 149 respectively with clustering found at the district level; v) chickens were exposed to the 150 ND vaccine strains caused by spent hens from commercial operations that were being sold to rural farmers by traders and released into rural settings; vi) AI ELISA-positive samples were tested using HIs against the H5, H6 and H7-subtypes, but only H6-specific antibodies were detected (H6N2). Since these viruses can mutate and reassort among