Using value chain and trade networks in the Eastern Cape Province of South Africa, as a basis for targeted rural chicken surveillance

Despite the benefits of rural chickens in the Eastern Cape Province (ECP) of South Africa, this sector is still underdeveloped and poorly surveyed for poultry diseases. The lack of a sustainable poultry disease surveillance system coupled with communities and practices where the interactions between birds are high, emphasize the need for targeted surveillance of chicken diseases in the province. However, to set up such a system requires knowledge of the value chain and trade networks. Consequently, a survey, which involved a rural chicken value chain analysis that also included an assessment of trading practices to identify biosecurity hotspots and an identification of barriers to market entry for rural farmers was conducted. Secondly, a social network analysis of chicken movements in the province was carried out to identify trade hubs that could be targeted for disease surveillance based on their centrality within the network and their size and influence within their ego networks. Traders and their transport vehicles were identified as biosecurity hotspots that could be targeted for disease surveillance within the chain. Social network analysis identified three municipalities viz. Umzimvubu, King Sabata Dalindyebo (KSD) and Enoch Mgijima as trade hubs where interaction between rural chickens occurs and resources can be focused. The movement of spent hens from commercial operations that are transported over long distances and distributed in the rural areas and townships were a major risk for spread of poultry diseases. This is the first study to formally describe chicken trade networks within the province and the surrounding region. Its findings provide a model for cost effective targeted surveillance in the ECP and similar resource poor regions of the world. The study also provides insight into the profitability of rural chickens and a possible contribution to job creation and poverty alleviation once the barriers to market entry are lifted.

A review of pig and poultry diseases in the Eastern Cape Province of South Africa, 2000-2020

The informal poultry and pig sector in the Eastern Cape Province (ECP) of South Africa is of significant socio-economic importance as it sustains livelihoods and ensures food security; yet little is known about the distribution and prevalence of infectious and zoonotic diseases in this region. This paper reviews data published for pig and poultry diseases in the province during the last 20 years (2000-2020). The review included relevant published papers identified by a computerised 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 Organisation for Animal Health (OIE) via the World Animal Health Information Database (WAHID) interface and laboratory records. A publication was considered eligible if it included qualitative or quantitative information on any disease affecting pigs and poultry including zoonosis. The search retrieved 174 publications, of which 26 were relevant. The review found that Newcastle disease (ND), coccidiosis and fowl pox (FP) were the most reported avian diseases in the national database, whereas avian infectious bronchitis (AIB), ND and highly pathogenic avian influenza (HPAI) were the most reported diseases in the OIE database. Classical swine fever (CSF) was the most reported pig disease in both databases. The retrieved literature on pig and poultry diseases was scarce and no longer up to date, providing decision makers with little information. The review identified important zoonotic diseases that require further studies yet failed to find information on important neglected diseases like leptospirosis.

A study of rural chicken farmers, diseases and remedies in the Eastern Cape province of South Africa

The source of emerging diseases and antimicrobial resistance is of increasing interest to epidemiologists. This paper looks at village chickens as such a source. In addition, infectious diseases constitute a major challenge to the growth and profitability of the rural poultry sector in Sub-Saharan Africa. A serological survey was conducted to estimate the apparent seroprevalence of selected chicken diseases in the Eastern Cape Province of South Africa alongside a sociological survey of poultry farmers and the remedies most commonly used to prevent diseases in their flocks. Sera collected from village chickens (n = 1007) in the province were screened for specific antibodies against Newcastle disease (ND), avian influenza (AI), avian infectious bronchitis (IB) and Mycoplasma gallisepticum (MG). The overall seroprevalence of ND, AI, IB and MG in the province was found to be 69.2 % (95 % CI 51.9-86.5%); 1.8 % (95 % CI 0.2-3.4%); 78.5 % (95 % CI 74.9-82%) and 55.8 % (95 % CI 41.3-70.3%) respectively with clustering found at the District level. Cross hemagglutination inhibition (HI) tests indicated that the chickens were exposed to the ND vaccine. AI ELISA-positive samples were tested using HIs against the H5, H6 and H7-subtypes, but only H6-specific antibodies were detected. Avian influenza strains shared the common ancestor responsible for the 2002 chicken outbreak in KwaZulu-Natal Province. The majority of chicken farmers 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, Aloe plant (Aloe ferox Mill.) or ikhala (Xhosa) was the most commonly used product (28.23 %) for preventing and reducing mortalities among village chickens. The findings stress the importance of village chickens as a substitute for social welfare and highlight the exposure of village chickens to important chicken pathogens. The economic impact of these pathogens on the development of this sub-sector needs further investigation. Village chickens are a potential source of virulent Newcastle disease virus (NDV) because of the lack of vaccination and biosecurity. They may serve as amplification hosts which increases the probability that virulent NDV could spill over into commercial poultry flocks due to large amounts of circulating virus. The zoonotic threat of circulating H6N2 viruses raise concern due to their mutation and reassortment among chickens and a potential movement of infected birds within the province. Finally, the use of antibiotics by untrained chicken farmers constitute another major concern as it could serve as a source of antimicrobial resistance (AMR).

The Incursion and Spread of Highly Pathogenic Avian Influenza H5N8 Clade 2.3.4.4 Within South Africa

The report of a mass die-off of white-winged terns (Chlidonias leucopterus) along the shores of Lake Victoria in Uganda in January 2017 was a warning that highly pathogenic avian influenza (HPAI) H5N8 clade 2.3.4.4 had entered the avian populations of the African Rift Valley. In early June 2017, Zimbabwe reported an outbreak of the virus in commercial breeder chickens near Harare, and on June 19, 2017, the first case of HPAI H5N8 was confirmed in a broiler breeder operation near Villiers, Mpumalanga Province, South Africa, representing the first ever notifiable influenza in gallinaceous poultry in South Africa. Forty viruses were isolated from wild birds, backyard hobby fowl, zoo collections, commercial chickens, and commercial ostriches over the course of the outbreak and full genomes were sequenced and compared to determine the epidemiologic events in the introduction and spread of clade 2.3.4.4 H5N8 across the country. We found that multiple virus variants were involved in the primary outbreaks in the north-central regions of South Africa, but that a single variant affected the southernmost regions of the continent. By November 2017 only two of the nine provinces in South Africa remained unaffected, and the layer chicken industry in Western Cape Province was all but decimated. Two distinct variants, suggesting independent introductions, were responsible for the first two index cases and were not directly related to the virus involved in the Zimbabwe outbreak. The role of wild birds in the incursion and spread was demonstrated by shared recent common ancestors with H5N8 viruses from West Africa and earlier South African aquatic bird low pathogenicity avian influenza viruses. Improved wild bird surveillance will play a more critical role in the future as an early warning system.

Avian Viral Pathogens in Swallows, Zimbabwe : Infectious Diseases in Hirundinidae: A Risk to Swallow?

We sampled 417 swallows in a wetland ecosystem of Zimbabwe in February 2010 and October 2011. RT-PCR tests revealed circulation of avian paramyxovirus type I, avian influenza and West Nile disease viruses in these populations. We discuss the relevance of these findings in relation to what is known on the epidemiology of these viruses in these hosts and in relation to the host ecology. We conclude with recommendations to focus more research on Passeriformes in disease ecology and in particular on the hirundinidae family.

Tracing the origins of genotype VIIh Newcastle disease in southern Africa

It is widely accepted that Newcastle disease is endemic in most African countries, but little attention has been afforded to establishing the sources and frequency of the introductions of exotic strains. Newcastle disease outbreaks have a high cost in Africa, particularly on rural livelihoods. Genotype VIIh emerged in South-East Asia and has since caused serious outbreaks in poultry in Malaysia, Indonesia, southern China, Vietnam and Cambodia. Genotype VIIh reached the African continent in 2011, with the first outbreaks reported in Mozambique. Here, we used a combination of phylogenetic evidence, molecular dating and epidemiological reports to trace the origins and spread of subgenotype VIIh Newcastle disease in southern Africa. We determined that the infection spread northwards through Mozambique, and then into the poultry of the north-eastern provinces of Zimbabwe. From Mozambique, it also reached neighbouring Malawi and Zambia. In Zimbabwe, the disease spread southward towards South Africa and Botswana, causing outbreaks in backyard chickens in early-to-mid 2013. In August 2013, the disease entered South Africa's large commercial industry, and the entire country was infected within a year, likely through fomites and the movements of cull chickens. Illegal poultry trading or infected waste from ships and not wild migratory birds was the likely source of the introduction to Mozambique in 2011.

A retrospective study and predictive modelling of Newcastle Disease trends among rural poultry of eastern Zambia

Newcastle Disease (ND) is a highly infectious disease of poultry that seriously impacts on food security and livelihoods of livestock farmers and communities in tropical regions of the world. ND is a constant problem in the eastern province of Zambia which has more than 740 000 rural poultry. Very few studies give a situational analysis of the disease that can be used for disease control planning in the region. With this background in mind, a retrospective epidemiological study was conducted using Newcastle Disease data submitted to the eastern province headquarters for the period from 1989 to 2014. The study found that Newcastle Disease cases in eastern Zambia followed a seasonal and cyclic pattern with peaks in the hot dry season (Overall Seasonal Index 1.1) as well as cycles every three years with an estimated provincial incidence range of 0.16 to 1.7% per year. Annual trends were compared with major intervention policies implemented by the Zambian government, which often received donor support from the international community during the study period. Aid delivered through government programmes appeared to have no major impact on ND trends between 1989 and 2014 and reasons for this are discussed. There were apparent spatial shifts in districts with outbreaks over time which could be as a result of veterinary interventions chasing outbreaks rather than implementing uniform control. Data was also fitted to a predictive time series model for ND which could be used to plan for future ND control. Time series modelling showed an increasing trend in ND annual incidence over 25 years if existing interventions continue. A different approach to controlling the disease is needed if this trend is to be halted. Conversely, the positive trend may be a function of improved reporting by farmers as a result of more awareness of the disease.

Molecular analysis of the 2011 HPAI H5N2 outbreak in ostriches, South Africa

The third outbreak of highly pathogenic avian influenza (HPAI) H5N2 in less than seven years affected ostriches of South Africa's Western Cape during 2011. Twenty farms tested PCR positive for the presence of HPAI H5N2 between March and November 2011. Three HPAI H5N2 (AI2114, AI2214, AI2512) and 1 H1N2 (AI2887) viruses were isolated during this period, but H6N2 and H1N2 infections of ostriches were also confirmed by PCR. HPAI H5N2 isolate AI2114 produced an intravenous pathogenicity index (IVPI) score of 1.37 in chickens whereas isolate AI2214 produced an IVPI score of 0.8. The former virus had an additional, predicted N-linked glycosylation site at position 88 of the hemagglutinin protein as well as an E627K mutation in the PB2 protein that was lacking from AI2214. Four variations at HA0 were detected in the PCR-positive cases. Phylogenetically, the branching order of outbreak strains indicated a lack of reassortment between outbreak strains that implied a single outbreak source and a wild duck origin for the progenitor outbreak strain. The 2011 outbreak strains had no genetic relationships to the previous 2004 and 2006 HPAI H5N2 outbreak viruses. Molecular clock analysis based on the N2 neuraminidase genes estimated a recent common ancestor for the outbreak tentatively dated at September 2010. Deep sequencing results of 16 clinical PCR-positive samples yielded data in the range of 573 to 12,590 base pairs (bp), with an average of 4468 bp of total genomic sequence recovered per sample. This data was used to confirm the lack ofreassortment and to assign samples into one of two epidemiologic groups to support epidemiologic tracing of the spread of the outbreak. One farm (no. 142), thought to have played a major epidemiologic role in the outbreak, was confirmed by deep sequencing to contain a mix of both epidemiologic virus groups.

Understanding the ecological drivers of avian influenza virus infection in wildfowl: a continental-scale study across Africa

Despite considerable effort for surveillance of wild birds for avian influenza viruses (AIVs), empirical investigations of ecological drivers of AIV prevalence in wild birds are still scarce. Here we used a continental-scale dataset, collected in tropical wetlands of 15 African countries, to test the relative roles of a range of ecological factors on patterns of AIV prevalence in wildfowl. Seasonal and geographical variations in prevalence were positively related to the local density of the wildfowl community and to the wintering period of Eurasian migratory birds in Africa. The predominant influence of wildfowl density with no influence of climatic conditions suggests, in contrast to temperate regions, a predominant role for inter-individual transmission rather than transmission via long-lived virus persisting in the environment. Higher prevalences were found in Anas species than in non-Anas species even when we account for differences in their foraging behaviour (primarily dabbling or not) or their geographical origin (Eurasian or Afro-tropical), suggesting the existence of intrinsic differences between wildfowl taxonomic groups in receptivity to infection. Birds were found infected as often in oropharyngeal as in cloacal samples, but rarely for both types of sample concurrently, indicating that both respiratory and digestive tracts may be important for AIV replication.

Efficacy of a genotype 2 Newcastle disease vaccine (Avinew®) against challenge with highly virulent genotypes 5d and 3d

Since 2002, following its introduction, the lineage 5d Newcastle disease virus (so-called Goose paramyxovirus -GPMV) strain has caused numerous disease outbreaks among commercial and backyard poultry in South Africa, raising questions about the ability of commercially available Newcastle disease vaccines to fully protect poultry against the strain. This study aimed to determine whether there are differences in the level of protection offered by Avinew® Newcastle disease vaccine against GPMV virus as compared with a 3d Newcastle disease virus isolated in South Africa in 1993 (Rainbow challenge virus - RCV) strain. Six groups of 10-day-old, specific pathogen-free chickens were vaccinated with doses of 103.0, 104.5 and 106.0 EID50 of Avinew® vaccine and challenged at 4 weeks of age intramuscularly at a dose of 105.3EID50/ 0.2 mℓ/bird of GPMV and RCV. No statistically significant difference could be found in the protection offered by Avinew® vaccine against GPMV as compared to RCV challenge. The protection offered against the ND challenge was found to be dose dependent. At the recommended field dose of 106.0 EID50 the vaccine gave 100 % protection from mortality against both the challenge viruses, but not against infection and replication of the viruses, as gross lesions were evident even in apparently healthy birds that survived the challenge. The protective dose (PD90) of the Avinew® vaccine against GPMV challenge was calculated at 104.38 and against that of RCV at 104.43.

A rapid and sensitive real-time reverse transcription PCR for the pathotyping of South African H5N2 avian influenza viruses

A Fluorescence resonance energy transfer (FRET) real-time reverse-transcription (rRT-PCR) assay was developed that distinguishes stains of South African and European highly pathogenic (HPAI) from low pathogenicity (LPAI) H5 avian influenza viruses in the absence of virus isolation, irrespective of the length of insertion at the hemagglutinin cleavage site (H0). The assay was used to pathotype H5-type viruses detected by rRT-PCR in ostrich tracheal swabs collected during the 2006 HPAI H5N2 outbreak in the Western Cape Province.

Characterization of pigeon paramyxoviruses (Newcastle disease virus) isolated in South Africa from 2001 to 2006

Pigeon paramyxovirus type 1 (PPMV-1), a variant of Newcastle disease virus that primarily affects doves and pigeons has been isolated in South Africa since the mid-1980s. Phylogenetic evidence indicates that pigeon paramyxovirus type 1 viruses were introduced into South Africa on multiple occasions, based on the presence of two separate lineages, 4bi and 4bii, that have been circulating in Europe and the Far East since the early 1990s. During 2006, a PPMV-1 virus was isolated from an African ground hornbill (Bucorvus leadbeateri) which became acutely infected with PPMV-1 and died, probably after scavenging off infected dove carcasses in the region, since a closely-related PPMV-1 strain was also isolated from doves collected nearby. The hornbill isolate had ICPI and MDT values characteristic of PPMV-1 strains. The threat of PPMV-1 to poultry production and biodiversity in southern Africa highlights the importance of monitoring the spread of this strain.

Phylogenetic analysis of low-pathogenicity avian influenza H6N2 viruses from chicken outbreaks (2001-2005) suggest that they are reassortants of historic ostrich low-pathogenicity avian influenza H9N2 and H6N8 viruses

Low-pathogenicity (LPAI) and high-pathogenicity (HPAI) avian influenza viruses are periodically isolated from South African ostriches, but during 2002 the first recorded outbreak of LPAI (H6N2) in South African chickens occurred on commercial farms in the Camperdown area of KwaZulu/Natal (KZN) Province. Sequence analysis of all eight genes were performed and phylogenetic analysis was done based on the hemagglutinin and neuraminidasc sequences. Results from phylogenetic analyses indicated that the H6N2 chicken viruses most likely arose from a reassortment between two South African LPAI ostrich isolates: an H9N2 virus isolated in 1995 and an H6N8 virus isolated in 1998. Two cocirculating sublineages of H6N2 viruses were detected, both sharing a recent common ancestor. One of these sublineages was restricted to the KZN province. The neuraminidase gene contained a 22-amino acid deletion in the NA-stalk region, which is associated with adaptation to growth in chickens, whereas the other group, although lacking the NA-stalk deletion, spread to commercial farms in other provinces. The persistence of particular H6N2 types in some regions for at least 2 yr supports reports from Asia and southern California suggesting that H6N2 viruses can form stable lineages in chickens. It is probable that the ostrich H6N8 and H9N2 progenitors of the chicken H6N2 viruses were introduced to ostriches by wild birds. Ostriches, in which AI infections are often subclinical, may serve as mixing vessels for LPAI strains that occasionally spill over into other poultry.

Detection of a North American lineage H5 avian influenza virus in a South African wild duck

An H5-coinfection of a sample from wild ducks from which an H3N8 virus was isolated in 2004 was detected by reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis of the partial H5 gene revealed that the strain was of low pathogenicity according to the amino acid sequence PQRTGLF at the Ho cleavage site. Phylogenetic analysis demonstrated that the partial H5 gene sequence fell within the American H5 lineage and shared 99.6% nucleotide sequence identity with the A/mallard duck/ALB/57/1976 (H5N2) strain isolated in 1976. Interregional transmission of influenza virus genes has been reported occasionally, although this is the first report from South Africa, where other influenza viruses have always had Eurasian origins.

Phylogenetic analyses of genes from South African LPAI viruses isolated in 2004 from wild aquatic birds suggests introduction by Eurasian migrants

In 2004, South Africa experienced its first recorded outbreak of a highly pathogenic notifiable avian influenza (HPNAI) viral strain of the H5N2 subtype in ostriches in the Eastern Cape province. The traditional ostrich-farming areas in the Western Cape province report almost yearly outbreaks of low pathogenicity avian influenza (LPAI) in ostriches, which is attributed to introduction by wild birds and certain climatic patterns. During the winter of 2004, LPAI H3N8, H4N8, H5N2 and H5N1 avian influenza viruses were isolated from wild aquatic birds. All eight genes of the H3N8, H4N8 and H5N1 viruses were analysed. The results show that the H5N1 virus does not belong to the HPAI Z/Z+N genotype currently circulating in Asia, but that the most recent common ancestors are Russian H5N2 and H5N3 viruses. The N1 gene lacks the stalk deletion associated with virulence. Internal genes probably originate from a pool containing Chinese, Middle Eastern and Italian viruses. The South African H3N8 and H4N8 viruses appear to have derived their genes from an ecosystem where Asian H5N1, H6N9 and H9N2, Russian H4, and Danish H3N8 viruses have been circulating since 1997. All three viruses share recent nucleoprotein common ancestors with the German and Dutch HPNAI H7N7 viruses from 2003. The diverse pool of genes from which local viruses are derived suggests that reassortment occurred at the Siberian breeding grounds where migratory paths cross, or within the South African ecosystem. This data highlights the importance of surveillance in aquatic migratory birds, particularly members of the Charadriidae, for their potential roles in the introduction of avian diseases to South African poultry and especially ostriches in the case of avian influenza.

Characterization of a pigeon paramyxovirus (PPMV-1) isolated from chickens in South Africa : research communication

A paramyxovirus with a thermostability of 60 min (typical of velogenic viruses) and a mean death time of > 90 h (typical of lentogenic viruses) was isolated from layers near Mooi River, South Africa. Our results, based on comparative nucleotide sequence data indicated that the virus is pigeon paramyxovirus 1 (PPMV-1), a variant of Newcastle disease virus. The F0 cleavage site contains a 112RRKKRF117 motif, and the virus had 98 % sequence identity with PPMV-1 strains from the Far East. PPMV-1 was last reported in South Africa during the 1980s, with this being the first report of PPMV-1 isolated from chickens in South Africa.

A phylogenetic study of South African Newcastle disease virus strains isolated between 1990 and 2002 suggests epidemiological origins in the Far East

Genetic comparisons were made of the fusion protein sequences of 155 Newcastle disease virus isolates collected in South Africa between 1990 and 2002. Their evolutionary relationships and origins are described. All of the lentogenic field isolates were shown to be derived from commercial vaccines. No true South African lentogenic wild type strain was identified. Furthermore, it was shown that almost all mesogenic isolates had avirulent F(0) cleavage site sequences. Three major epizootics occurred in South Africa during the period of this study. The first outbreak (1990/1991) was caused by viruses endemic to South Africa since the 1960's (genotype VIII) but were occasionally also isolated in 2000. Genotype VIIb viruses, implicated in the severe outbreaks during 1993/1994, persisted until 1999. Genotype VIId viruses, responsible for the most recent outbreak in 1999/2000, had their origins in the Far East like those of the two previous outbreaks.

Comparative sequence analysis of the South African vaccine strain and two virulent field isolates of Lumpy skin disease virus

The genomic sequences of 3 strains of Lumpy skin disease virus (LSDV) (Neethling type) were compared to determine molecular differences, viz. the South African vaccine strain (LW), a virulent field-strain from a recent outbreak in South Africa (LD), and the virulent Kenyan 2490 strain (LK). A comparison between the virulent field isolates indicates that in 29 of the 156 putative genes, only 38 encoded amino acid differences were found, mostly in the variable terminal regions. When the attenuated vaccine strain (LW) was compared with field isolate LD, a total of 438 amino acid substitutions were observed. These were also mainly in the terminal regions, but with notably more frameshifts leading to truncated ORFs as well as deletions and insertions. These modified ORFs encode proteins involved in the regulation of host immune responses, gene expression, DNA repair, host-range specificity and proteins with unassigned functions. We suggest that these differences could lead to restricted immuno-evasive mechanisms and virulence factors present in attenuated LSDV strains. Further studies to determine the functions of the relevant encoded gene products will hopefully confirm this assumption. The molecular design of an improved LSDV vaccine is likely to be based on the strategic manipulation of such genes.