Epidemiology of African swine fever in Nigeria

African swine fever (ASF) is a highly contagious transboundary viral infection of domestic pigs that has serious socio-economic implications on people’s livelihood, international trade and food security. It is still a major limitation to profitable pig production and presently, it is threatening the pig industry internationally with current outbreaks in the Russian federation and the Caucasus. Since 1996, the disease has made major incursions into the West African sub-region. In this study, a combination of classical epidemiologic (statistical), economic, laboratory (serological, virological and molecular) and evidence-based tools were used to determine the prevalence of ASF in Nigeria, map the temporal situation of the virus, estimate the economic implications of infection with justification of alternative control (biosecurity), compare and contrast the virulence genes (Thymidine kinase, TK) and finally evaluate the effectiveness of ethnoveterinary preparations used in the management of ASF. Nine percent (9%) of serum samples and 48% of tissue samples tested were positive for ASF virus antibody and genome, respectively. Areas with high pig-related activities (marketing, consumption and farming) have higher prevalences compared with areas with less pig activities. Farm-gate buyers, marketing systems and transport of untested pigs within the country appeared to assist with the circulation of the virus. Using the financial model of partial budgeting and benefit-cost analysis, ASF outbreak in a 122-sow unit may lead to a loss of up to ZAR7,475,867.27 (US$910,836.70) in a single year while the implementation of biosecurity and its effective monitoring can prevent these losses with certain other social benefits and give a benefit-cost ratio of approximately 29 in return, but the cost of its implementation may result in a 9.70% less annual profit. Since the identification of factors that supports infection on pig farms in the sub-region remains the key component in the development of a risk-based approach to control the disease, most plausible risk factors and biosecurity measures previously identified were analysed in this study with a univariable/multivariable conditional logistic regression analytic models. Presence of an abattoir in a pig farming community (OR = 8.20; P < 0.001) and the presence of an infected pig farm in the neighbourhood (OR = 3.26; P = 0.02) were significant risk factors. There was a marginally significant negative association (protective) between risk of ASF infection and sharing farm tools and equipment (OR = 0.35; P = 0.05). For the biosecurity measures evaluated, food and water control (OR = 0.14; P < 0.001), separation/isolation of sick pigs (OR = 0.14; P = 0.004) and washing and disinfection of farm equipment and tools (OR = 0.27; P = 0.02) were negatively associated (protective) with ASF infection. Consultation and visits by veterinarian/paraveterinarians when animals were sick (OR = 8.11; P = 0.002), and pest and rodent control were positively associated with ASF infection of Nigerian farms (OR = 4.94; P = 0.002). The leaf, root and stem portions of Ancistrocladus korupensis possessed some chemical compounds with antiviral potentials and extracts and fractions from the plant showed very good antiviral (virucidal) activities in-vitro against ASF virus (NIG/99). It also has certain cytotoxic principles and narrow therapeutic index. Further studies on the maximization of the ethnoveterinary potentials of the plant invivo and in-vitro while reducing its cytotoxic potentials will be needed. Using molecular characterization, similar unresolved topologies were observed within the European, South America, Caribbean and West African (ESAC-WA) genotype and the mean character distances on the coded data set revealed least possible loss of information that would have otherwise been ignored in pairwise- or complete- deletion distance analysis. The size of the coding ORF for the TK protein varies between isolates but the majority of isolates code for a protein of 196 amino acids. These isolates comprise of viruses from Europe, West, Central and Southern Africa. A smaller TK gene product of 185 and 194 amino acids, caused due to a frameshift mutation at nucleotide position 561 in many of the East African isolates resulting in stop codons immediately thereafter or further downstream (nucleotide position 571 in Malawi 3). Despite the smaller TK protein product size, certain nonsense insertions of differing length were responsible for some considerably larger TK-PCR products. This TK protein heterogeneity is unexpected in an enzyme with such an important function and these size differences may have an effect on virulence. It is concluded that strains from southern Africa may have a shared evolutionary history with strains of the ESAC-WA genotype but may differ from the evolutionary lineage from East Africa. It is also suggested that a link exist between the sylvatic cycle, domestic tick cycle and the truncated TK products. Finally, putting in place a comprehensive routine surveillance and testing system to rapidly eliminate all pigs in infected farms, reorganization of the market and transportation systems for pigs, implementation of carefully planned on-farm biosecurity protocols, and giving consideration to the option of compensation to encourage reporting of outbreaks will possibly achieve a significant reduction in high ASF prevalence in Nigeria. It will be desirable to eliminate certain risky farm-related practices and behaviours (e.g the removal of all pig abattoir from within the pig communities, isolation of infected neighbourhood farm) while entrenching farm-level biosecurity as these appear to be the key to controlling ASF within the subregion. In conclusion, the outcomes of this research can be used to plan long-term strategies for countries like Nigeria, and assist the ASF unaffected countries that are at risk of infection to organize and secure their animal (pig) resources, so that Africa can be free from the significant effects of ASF and explore options of international markets.Thesis (PhD)--University of Pretoria, 2012.Zoology and EntomologyUnrestricte

Molecular and spatial-temporal epidemiology of highly pathogenic notifiable avian influenza (HPNAI) H5N1 in Nigeria

Highly pathogenic notifiable avian influenza (HPNAI) is a disease caused by influenza A virus. It is frequently fatal in poultry. Since late 2003, disease outbreaks caused by the Asian strains of HPAI H5N1 virus have ravaged the poultry industry with the death of over 200 million birds. The epidemic has spread from Asia to Europe and more recently to Africa. To date, more than 200 human fatalities have occurred. A clear understanding of the full epidemiology of the disease at the genetic and spatial/temporal level is critical for the management, control and eventual eradication of the virus. In this study, modern tools of molecular epidemiology (Reverse-transcriptase polymerase chain reaction (RT-PCR), molecular characterization and phylogenetic analyses), Geographical Information Systems (GIS) and remote sensing, and other epidemiological tools were used to explore the outbreak of HPNAI in Nigeria. The molecular and spatial analyses both concluded that Nigeria was infected with multiple infections. The spread of primary outbreaks, which affected mainly sectors 2 and 3 of the poultry industry as described by Food and Agricultural Organisation of the United Nations, were strongly linked to trades, live bird markets, inappropriate disposal of carcasses and poorly implemented control measures. This work did not find a strong correlation between wild birds and HPNAI H5N1 in Nigeria. Some of the analyzed viruses showed genetic drift, and the implications of these for future epidemiology and ecology of avian influenza in Africa will need further evaluation. The option of vaccination and its implications were adjudged good, and its shortcomings were highlighted. Community initiative at fighting emergency diseases like HPNAI H5N1 was similarly advocated. The financial losses to the Nigerian poultry industry were estimated at around $680 million. The risk of the spread of infection was assessed using ecological niche modeling and the whole of West Africa is at risk of infection, should no concrete action be taken to halt the spread. In conclusion, useful suggestions were proffered to affected countries like Nigeria, and unaffected countries that are at risk of infection, so that Africa can be safe from the scourge of HPNAI H5N1.Dissertation (MSc)--University of Pretoria, 2008.Production Animal Studiesunrestricte

Statistical methods for comparing test positivity rates between countries : which method should be used and why?

The test positivity (TP) rate has emerged as an important metric for gauging the illness burden due to COVID-19. Given the importance of COVID-19 TP rates for understanding COVID-related morbidity, researchers and clinicians have become increasingly interested in comparing TP rates across countries. The statistical methods for performing such comparisons fall into two general categories: frequentist tests and Bayesian methods. Using data from Our World in Data (ourworldindata.org), we performed comparisons for two prototypical yet disparate pairs of countries: Bolivia versus the United States (large vs. small-to-moderate TP rates), and South Korea vs. Uruguay (two very small TP rates of similar magnitude). Three different statistical procedures were used: two frequentist tests (an asymptotic z-test and the ‘N-1’ chi-square test), and a Bayesian method for comparing two proportions (TP rates are proportions). Results indicated that for the case of large vs. small-to-moderate TP rates (Bolivia versus the United States), the frequentist and Bayesian approaches both indicated that the two rates were substantially different. When the TP rates were very small and of similar magnitude (values of 0.009 and 0.007 for South Korea and Uruguay, respectively), the frequentist tests indicated a highly significant contrast, despite the apparent trivial amount by which the two rates differ. The Bayesian method, in comparison, suggested that the TP rates were practically equivalent—a finding that seems more consistent with the observed data. When TP rates are highly similar in magnitude, frequentist tests can lead to erroneous interpretations. A Bayesian approach, on the other hand, can help ensure more accurate inferences and thereby avoid potential decision errors that could lead to costly public health and policy-related consequences.https://www.elsevier.com/locate/ymeth2022-03-18hj2021Veterinary Tropical Disease

COVID-19 pandemic impacted food security and caused psychosocial stress in selected states of Nigeria

SUPPLEMENTARY MATERIALS : TABLE S1: Economic and livelihood data and food-related issues for respondents psychosocial and food security-related impacts of COVID-19, Nigeria; TABLE S2: Psychological stress and self-rated quality of life of respondents per socioeconomic earning category due to impact of COVID-19.DATA AVAILABLITY STATEMENT : The data used in this study are available upon reasonable request from the corresponding author.The COVID-19 disease has infected many countries, causing generalized impacts on different income categories. We carried out a survey among households (n = 412) representing different income groups in Nigeria. We used validated food insecurity experience and socio-psychologic tools. Data obtained were analyzed using descriptive and inferential statistics. The earning capacities of the respondents ranged from 145 USD/month for low-income earners to 1945 USD/month for high-income earners. A total of 173 households (42%) ran out of food during the COVID-19 pandemic. All categories of households experienced increasing dependency on the general public and a perception of increasing insecurity, with the high-income earners experiencing the greatest shift. In addition, increasing levels of anger and irritation were experienced among all categories. Of the socio-demographic variables, only gender, educational level of the household head, work hours per day, and family income based on society class were associated (p < 0.05) with food security and hunger due to the COVID-19 pandemic. Although psychological stress was observed to be greater in the low-income earning group, household heads with medium and high family income were more likely to have satisfactory experiences regarding food security and hunger. It is recommended that socio-economic groups should be mapped and support systems should target each group to provide the needed support in terms of health, social, economic, and mental wellness.http://www.mdpi.com/journal/ijerphVeterinary Tropical DiseasesSDG-02:Zero HungerSDG-03:Good heatlh and well-bein

Determining the adrenocortical activity as a measure of stress in domestic pigs (Sus scrofa domesticus) based on salivary and faecal analysis

Domestic pigs are subjected to farm management procedures, some of which might be perceived as causing stress and therefore may have welfare concerns. When confronted with a stressor, animals display a response that consists of a suite of physiological and behavioural alterations to restore homeostasis. Physiologically, the response is usually determined using glucocorticoid concentrations (GC) albeit invasively, with the disadvantage of a possible handling-induced stress response. To date, no non-invasive method exists for determining stress-related responses in pigs. This study aimed to examine the suitability of enzyme-immunoassays (EIAs) for determining GC concentrations in saliva and faeces of domestic pigs by performing an ACTH challenge. A total of 6 animals were studied with 4 receiving 10µg/kg of Synacthen® (Novartis, South Africa Pty Ltd) and the remaining 2 receiving 0.5 ml physiologic saline. Baseline salivary glucocorticoid (sGC) concentrations of 2.38±1.83ng/ml (mean±SEM) increased by six-fold (14.03±6.83 ng/ml) within 40-90 minutes after administration of ACTH (P < 0.0001) and the elevated salivary cortisol levels were maintained for up to nine hours. Administration of saline caused no significant differences in sGC concentrations (P = 0.82). Similarly, baseline faecal glucocorticoid metabolite (fGCM) level of 235±46μg/g rose significantly up to 393±164μg/g within 36 hours post ACTH administration (P < 0.0001). No significant difference was found between baseline and post saline administration (P = 0.57). Significantly higher sGC concentrations were found in samples collected in the morning compared to those collected in the afternoon, indicating a circadian rhythm. In terms of stability of fGCMs, post-defecation levels only changed by 4% over the course of 50h (P = 0.76). In conclusion, EIAs can be used to determine sGC and fGCM concentrations to assess adrenocortical function in pigs. FGCM levels are relatively stable for at least two days post-defecation, which facilitates field sample submissions.Poster presented at the University of Pretoria, Faculty of Veterinary Science Faculty Day, August 25, 2016, Pretoria, South Africa.ab201

Is a 10-sow unit economically sustainable? A profitability assessment of productivity amongst small-holder pig farmers, Mpumalanga, South Africa

The majority of small-holder pig farmers in Mpumalanga had between 1- and 10-sow herds. The main aim of this study is to evaluate the current government agricultural intervention (supply of 10 sows and a boar) in terms of technical and economic feasibilities and ascertain whether the small-scale pig value chain system alleviates poverty. Data were obtained from 220 randomly selected small-holder pig farmers using a semi-structured questionnaire. The results showed that 58% farrowed ≤ 10 piglets/born/sow/litter, 44.2% practiced no weaning method and many fed swill and leftovers alone (41.6%). Pair-wise association revealed that the feeding of commercial feeds had a relationship with pigs in relatively good to very good body condition. Pigs in poor body condition were positively correlated with the feeding of swill alone. The economic models for the 10-sow unit proved that pig farming is unprofitable if the current management and feeding systems that operate in the commercial industry are utilised. However, only through a combination of cooperative systems, benefits of economies of scale, reduction of preweaning mortalities and structured government inputs can pig production be profitable at this scale of production.UNISA M & D bursaryhttp://www.ojvr.orgam2016Production Animal Studie

Is a 10-sow unit economically sustainable? A profitability assessment of productivity amongst small-holder pig farmers, Mpumalanga, South Africa

The majority of small-holder pig farmers in Mpumalanga had between 1- and 10-sow herds. The main aim of this study is to evaluate the current government agricultural intervention (supply of 10 sows and a boar) in terms of technical and economic feasibilities and ascertain whether the small-scale pig value chain system alleviates poverty. Data were obtained from 220 randomly selected small-holder pig farmers using a semi-structured questionnaire. The results showed that 58% farrowed ≤ 10 piglets/born/sow/litter, 44.2% practiced no weaning method and many fed swill and leftovers alone (41.6%). Pair-wise association revealed that the feeding of commercial feeds had a relationship with pigs in relatively good to very good body condition. Pigs in poor body condition were positively correlated with the feeding of swill alone. The economic models for the 10-sow unit proved that pig farming is unprofitable if the current management and feeding systems that operate in the commercial industry are utilised. However, only through a combination of cooperative systems, benefits of economies of scale, reduction of preweaning mortalities and structured government inputs can pig production be profitable at this scale of production.UNISA M & D bursaryhttp://www.ojvr.orgam2016Production Animal Studie

Investigation of multidrug-resistant fatal colisepticaemia in weanling pigs

Escherichia coli is usually a benign commensal of the gut microflora. However, when E. coli acquires virulence genes it can multiply rapidly and cause disease through colonisation of the intestinal mucosa. Escherichia coli can become a significant pathogen in young pigs. We report an investigation of fatal colisepticaemia in weanling pigs from emerging farms where piglets and weaners were diarrhoeic and the mortality rate ranged between 15% and 70% in each litter. Faecal and tissue samples were processed for histopathology, bacteriology and molecular biology (multiplex and monoplex polymerase chain reaction) and we recovered enteroaggregative multidrug-resistant E. coli producing EAST-1 enterotoxin. An association between poor housing conditions and the observed cases was established and future management programmes were recommended to reduce the impact of such pathogens. Enteroaggregative E. coli is becoming a major problem in the pig industry. It therefore becomes necessary to establish the full impact of E. coli on the South African pig industry and to determine the geographic extent of the problem.http://www.ojvr.orgam2015ab201

Effectiveness of combined treatment using Spirulina and vitamin A against chronic arsenicosis in rats

Chronic arsenicosis remains a condition of public health concerns in many countries of the world and has been linked to many other diseases. This condition has been managed in humans using a combination of therapy with differing outcomes. We conducted a controlled experiment to assess the effect of chronic arsenicosis on hematological and biochemical changes in Long-Evans rats and to assess the protective role of Spirulina combined with vitamin A following experimental arsenicosis, using daily oral doses of sodium arsenite for 63 days. The values of SGOT (Serum glutamate oxaloacetate transaminase) and SC (Serum creatinine) increased significantly (P<0.01) in all the treated groups of rats (T1, T2, T3 and T4) compared to the control (T0) group, but Spirulina combined with Vitamin A produced values significantly comparable to the untreated control group. Whereas SGPT (Serum glutamate pyruvate transaminase) showed slight significance differences among the treatment groups, Spirulina combined with Vitamin A appeared most effective in managing arsenic treatment. Spirulina + Vitamin A increased the values of TEC, TLC and Hb (Total erythrocyte count, Total leukocyte count and Hemoglobin) against arsenic toxicity in rats but showed no significance differences. In conclusion, the combination of Spirulina and vitamin A were found more effective in the prevention of chronic arsenicosis in rat than using these substances (Spirulina or Vitamin A) alone.http://www.academicjournals.org/AJPPam201

Systematic review and meta-analyses of cases and deaths associated with highly pathogenic avian influenza H5N1 in humans and poultry

From 2003 to date (2015), confirmed highly pathogenic avian influenza (HPAI) H5N1 outbreaks in poultry and humans have been reported, however, certain quantitative parameters remain lacking. We obtained 846 reports of HPAI H5N1 outbreaks in poultry in Africa (2006–2015), and 844 reports in humans globally (2003–2015) from different databases. Data were filtered and analysed using meta-analyses. The outputs were generated for each country included in the study and for overall morbidities, mortalities and case fatalities (for poultry and humans). Approximately 11.6 million poultry were included in the analyses as susceptible with 1.9 million cases and 1.7 million deaths in poultry. In humans, 449 deaths were linked to influenza A H5N1 infections. For all poultry outbreaks in 2006–2015 in Africa, an overall mean apparent morbidity of 48.7% (n = 1 850 589) was estimated, with overall mean apparent mortality being 40.2% (n = 1 705 388) and overall mean case fatality rate (CFR) for HPAI H5N1 outbreaks in poultry being 86.4% (n = 1 705 388). In humans, the overall mean CFR for A H5N1 globally for 2003–2015 was 62.3% (n = 449). Indonesia, Egypt and Vietnam had higher proportions of all human deaths associated with the A H5N1 and Egypt had a significant age–sex bias. Improved reporting and effective quantitation remain key to understanding the characteristics of the virus.http://www.cabi.org/cabreviews/am2017Production Animal StudiesVeterinary Tropical DiseasesZoology and Entomolog