Folorunso Oludayo Fasina

Transmission dynamics and control of ebola virus disease outbreak in Nigeria, July to september 2014

We analyse up-to-date epidemiological data of the Ebola virus disease outbreak in Nigeria as of 1 October 2014 in order to estimate the case fatality rate, the proportion of healthcare workers infected and the transmission tree. We also model the impact of control interventions on the size of the epidemic. Results indicate that Nigeria’s quick and forceful implementation of control interventions was determinant in controlling the outbreak rapidly and avoiding a far worse scenario in this country.

Predictable ecology and geography of avian influenza (H5N1) transmission in Nigeria and West Africa

The emerging virus strain termed highly pathogenic H5N1 avian influenza (HP-H5N1) has spread widely in the past decade and is now the focus of considerable concern in several sectors. We tested the hypothesis that spatial distributions of veterinary and human HP-H5N1 cases are related to coarse-scale environmental features in West Africa. We used ecological niche models to associate Nigerian HP-H5N1 occurrences with 1 km resolution digital data layers summarizing parameters of surface reflectance and landform. Predictive challenges included anticipating the spatial distribution of (i) random subsamples and (ii) spatially and temporally stratified subsamples of Nigerian occurrence data, and (iii) more limited occurrence data from across West Africa. In almost all tests, we found that HP-H5N1 cases were occurring under predictable environmental conditions, suggesting that elements of the transmission cycle have some form of ecological determination, here measured as differences in land-surface reflectance and plant phenology through the year. Considerable additional work is needed to establish how these differences affect HP-H5N1 transmission.

Identification of risk factors associated with highly pathogenic avian influenza H5N1 virus infection in poultry farms, in Nigeria during the epidemic of 2006-2007.

We conducted a matched case-control study to evaluate risk factors for infection with highly pathogenic avian influenza (HPAI) H5N1 virus in poultry farms during the epidemic of 2006-2007 in Nigeria. Epidemiologic data were collected through the use of a questionnaire from 32 case farms and 83 control farms. The frequency of investigated exposure factors was compared between case and control farms by using conditional logistic regression analysis. In the multivariable analysis, the variables for (i) receiving visitors on farm premises (odds ratio [OR]=8.32; 95% confidence interval [CI]=1.87, 36.97; P<0.01), (ii) purchased live poultry/products (OR=11.91; 95% CI=3.11-45.59; P<0.01), and (iii) farm workers live outside the premises (OR=8.98; 95% CI=1.97, 40.77; P<0.01) were identified as risk factors for HPAI in poultry farms. Improving farm hygiene and biosecurity should help reduce the risk for influenza (H5N1) infection in poultry farms in Nigeria.

Molecular Diagnosis of African Swine Fever by a New Real-Time PCR Using Universal Probe Library

A highly sensitive and specific real-time PCR method was developed for the reliable and rapid detection of African swine fever virus (ASFV). The method uses a commercial Universal Probe Library (UPL) probe combined with a specifically designed primer set to amplify an ASFV DNA fragment within the VP72 coding genome region. The detection range of the optimized UPL PCR technique was confirmed by analysis of a large panel (n = 46) of ASFV isolates, belonging to 19 of the 22 viral p72 genotypes described. No amplification signal was observed when closely clinically related viruses, such as classical swine fever, or other porcine pathogens were tested by this assay. The detection limit of the UPL PCR method was established below 18 DNA copies. Validation experiments using an extensive collection of field porcine and tick samples (n = 260), coming from Eastern and Western African regions affected by ASF, demonstrated that the UPL PCR technique was able to detect over 10% more positive samples than the real-time TaqMan PCR test recommended in the OIE manual, confirming its superior diagnostic sensitivity. Clinical material collected during experimental infections with different ASFV p72 genotypes was useful for assuring both the capacity of the UPL PCR for an early viral DNA detection and the competence of the technique to be applied in any ASF diagnostic target sample. The reliability and robustness of the UPL PCR was finally verified with a panel of ASFV-infected clinical samples which was repeatedly tested at different times. Additionally, an internal control PCR assay was also developed and standardized using UPL probes within the endogenous β-actin gene. Finally, the complete study offers a new validated real-time PCR technique, by means of a standardized commercial probe, providing a simple, rapid and affordable test, which is ready for application in the routine diagnosis of ASF.

The cost–benefit of biosecurity measures on infectious diseases in the Egyptian household poultry

Increased animal intensification presents with increasing risks of animal diseases. The Egyptian household poultry is peculiar in its management style and housing and this present with particular challenges of risk of infection to both the flock and humans. Biosecurity remains one of the most important means of reducing risks of infection in the household poultry, however not much information is available to support its feasibility at the household level of production. In this study financial feasibilities of biosecurity were modeled and evaluated based on certain production parameters. Risks of particular importance to the household poultry were categorized and highly pathogenic avian influenza H5N1 was the most risky disease while people-related risk was the most important risk category. It was observed that basic biosecurity measures were applicable in the household poultry and it would be 8.45 times better to implement biosecurity than to do nothing against HPAI H5N1; 4.88 times better against Newcastle disease and 1.49 times better against coccidiosis. Sensitivity analyses proved that the household poultry project was robust and would withstand various uncertainties. An uptake pathway for basic biosecurity was suggested. The outcome of this work should support decisions to implement biosecurity at the household sector of poultry production.

Cost implications of African swine fever in smallholder farrow-to-finish units : economic benefits of disease prevention through biosecurity

African swine fever remains the greatest limitation to the development of the pig industry in Africa, and parts of Asia and Europe. It is especially important in West and Central African countries where the disease has become endemic. Biosecurity is the implementation of a set of measures that reduce the risk of infection through segregation, cleaning and disinfection. Using a 122-sow piggery unit, a financial model and costing were used to estimate the economic benefits of effective biosecurity against African swine fever. The outcomes suggest that pig production is a profitable venture that can generate a profit of approximately US

Molecular characterization and epidemiology of the highly pathogenic avian influenza H5N1 in Nigeria.

109,637.40 per annum and that an outbreak of African swine fever (ASF) has the potential to cause losses of up to US

Lessons from Nigeria : the role of roads in the geo-temporal progression of avian influenza (H5N1) virus

910,836.70 in a single year. The implementation of biosecurity and its effective monitoring can prevent losses owing to ASF and is calculated to give a benefit-cost ratio of 29. A full implementation of biosecurity will result in a 9.70% reduction in total annual profit, but is justified in view of the substantial costs incurred in the event of an ASF outbreak. Biosecurity implementation is robust and capable of withstanding changes in input costs including moderate feed price increases, higher management costs and marginal reductions in total outputs. It is concluded that biosecurity is a key to successful pig production in an endemic situation.

Avian influenza risk perception among poultry workers, Nigeria.

Avian influenza caused infection and spread throughout Nigeria in 2006. Carcass samples (lung, liver, spleen, heart, trachea and intestine) from the different regions of Nigeria were processed for virus isolation. Infective allantoic fluids were tested for avian influenza viruses (AIV) and Newcastle disease virus using monospecific antisera. Thirty-five isolates were generated and characterized molecularly using the haemagglutinin gene. The molecular analysis indicated that different sublineages of the highly pathogenic avian influenza (HPAI) H5N1 viruses spread throughout Nigeria. We compared the Nigerian isolates with others from Africa and results indicated close similarities between isolates from West Africa and Sudan. Some of the analysed viruses showed genetic drift, and the implications of these for future epidemiology and ecology of avian influenza in Africa require further evaluation. The spread of primary outbreaks was strongly linked to trade (legal and illegal), live bird markets, inappropriate disposal, and poorly implemented control measures. No strong correlation existed between wild birds and HPAI H5N1 in Nigeria.

Control versus no control: options for avian influenza H5N1 in Nigeria.

The daily progression of the 2006 (January-June) Nigerian avian influenza (AI H5N1) epidemic was assessed in relation to both spatial variables and the generation interval of the invading virus. Proximity to the highway network appeared to promote epidemic dispersal: from the first AI generation interval onwards > 20% of all cases were located at < 5 km from the nearest major road. Fifty-seven per cent of all cases were located 31 km from three highway intersections. Findings suggest that the spatial features of emerging infections could be key in their control. When the spatial location of a transmission factor is well known, such as that of the highway network, and a substantial percentage of cases (e.g. > 20%) are near that factor, early interventions focusing on transmission factors, such as road blocks that prevent poultry trade, may be more efficacious than interventions applied only to the susceptible population.