Seroprevalence Estimates of Q Fever and the Predictors for the Infection in Cattle, Sheep, and Goats in Nandi County, Kenya.

Q fever is an important worldwide zoonotic disease that affects almost all domestic animals, wildlife, and humans. The infection has both socio-economic and public health significance. A cross-sectional study was carried out to investigate the estimates of seroprevalence of Q fever and to determine the predictors of the infection in cattle, sheep, and goats in six wards of Nandi County. A total of 1,140 blood samples were collected from 366 households. Samples were drawn from 725 cattle (64%), 283 sheep (25%), and 132 goats (11%). Multistage sampling method was adopted. Serum samples were analyzed for antibodies to Coxiella burnetii using the indirect ELISA test. Results showed an overall animal seroprevalence of 5.614% (64/1140) for Q fever. In cattle, the seroprevalence was 8.138% (59/725) with CI 95% (2.8-18.23), 1.413% (4/283) for sheep CI 95% (1.0-7.78), and 0.758% (1/132) goats CI 95% (0.14-7.27). From the findings, Q fever was more prevalent in cattle (OR 7.26) than in sheep and goats. Animal species (p value 0.015, CI 95% OR 7.26) was the only potential predictors in the three considered species for the presence of Coxiella burnetii antibodies. Sex, age, breed, and production system had no statistical significant association for Q fever infection since p value was >0.005. In conclusion, the results demonstrated that cattle, sheep, and goats are widely exposed to Q fever organisms, and hence, it is an important zoonosis in Nandi County. Therefore, to address this "silent" disease, there is an urgent call for both veterinarians and medical personnel to jointly address prevention and control strategy through enhanced surveillance, public sensitization, and awareness creation under the one health concept. There is also a need for enhanced capacity for the diagnosis of Q fever in both animals and humans in Nandi County.

Challenging the highstand-dormant paradigm for land-detached submarine canyons.

Sediment, nutrients, organic carbon and pollutants are funnelled down submarine canyons from continental shelves by sediment-laden flows called turbidity currents, which dominate particulate transfer to the deep sea. Post-glacial sea-level rise disconnected more than three quarters of the >9000 submarine canyons worldwide from their former river or long-shore drift sediment inputs. Existing models therefore assume that land-detached submarine canyons are dormant in the present-day; however, monitoring has focused on land-attached canyons and this paradigm remains untested. Here we present the most detailed field measurements yet of turbidity currents within a land-detached submarine canyon, documenting a remarkably similar frequency (6 yr-1) and speed (up to 5-8 ms-1) to those in large land-attached submarine canyons. Major triggers such as storms or earthquakes are not required; instead, seasonal variations in cross-shelf sediment transport explain temporal-clustering of flows, and why the storm season is surprisingly absent of turbidity currents. As >1000 other canyons have a similar configuration, we propose that contemporary deep-sea particulate transport via such land-detached canyons may have been dramatically under-estimated.

Epidemic disease risks and implications for Veterinary Services.

Growth in the livestock sector is associated with heightened risk for epidemic diseases. The increasing spillover of new diseases from wildlife is being driven by wide-scale anthropogenic changes allowing for more frequent and closer wildlife-human and wildlife-livestock contacts. An increasing number of epidemics in livestock are associated with rapid transition of livestock systems from extensive to intensive, and local to global movement of livestock and their products through value chain networks with weak biosecurity. Major livestock epidemics in the past two decades have had substantial economic impacts, and the COVID-19 pandemic highlights the devastating socio-economic consequences that spillovers can have when not identified and controlled early in the process of emergence. This highlights the importance of Veterinary Services to integrated, whole-of-society efforts to control infectious diseases in animals. Emphasis within Veterinary Services must be placed on prevention and preparedness. The authors suggest four areas for continued improvement in Veterinary Services to meet this challenge. These are a) continued development of staff capacity for risk assessment and value chain analysis, together with improved policies and communication, b) appropriate adaptation of approaches to prevention and control in resource-poor settings, c) improved multi-sectoral and transboundary cooperation, which enables the sharing of resources and expertise, and d) systematic approaches that enable Veterinary Services to influence decisionmaking for trade, markets, business, public health, and livelihood development at the national and regional levels.

La croissance du secteur de l'élevage est associée à un risque accru de maladies épidémiques. Les changements anthropiques à grande échelle sont à l'origine du nombre croissant de maladies émergentes atteignant de nouvelles espèces réceptives (spillover) à partir de réservoirs sauvages, à la faveur de contacts plus fréquents et plus rapprochés entre la faune sauvage et les humains, d'une part, et entre la faune sauvage et les animaux domestiques, d'autre part. On considère qu'un nombre croissant d'épidémies affectant le bétail sont dues à la transition rapide des systèmes d'élevage extensif vers des systèmes intensifs, et aux mouvements du bétail et des produits de l'élevage de l'échelle locale à l'échelle mondiale par le biais de réseaux de chaînes de valeur dotés d'un faible niveau de biosécurité. Au cours des deux dernières décennies, d'importantes épidémies affectant le bétail ont eu un impact économique considérable ; en outre, la pandémie de COVID-19 a mis en évidence les conséquences socio-économiques dévastatrices des atteintes de nouvelles espèces réceptives par des agents pathogènes, lorsque ces maladies ne sont pas détectées et maîtrisées dès le processus d'émergence. Cela souligne l'importance cruciale des Services vétérinaires dans les efforts de lutte contre les maladies infectieuses chez les animaux, qui doivent être intégrés et mobiliser la société entière. Les Services vétérinaires doivent mettre un accent particulier sur la prévention et la préparation. Les auteurs proposent quatre aspects d'amélioration continue pour que les Services vétérinaires puissent relever ce défi. Il s'agit : a) du développement permanent des compétences des personnels vétérinaires en matière d'évaluation du risque et d'analyse des chaînes de valeur, et leur articulation avec de meilleures politiques et une communication plus performante ; b) une adaptation adéquate des méthodes de prévention et de contrôle dans les configurations faiblement dotées en ressources ; c) une meilleure coopération multisectorielle et transfrontalière afin de partager les ressources et les compétences ; d) des dispositifs systémiques permettant aux Services vétérinaires d'influencer les prises de décision en matière d'échanges internationaux, de marchés, de commerce, de santé publique et de développement des moyens de subsistance, à l'échelle nationale et régionale.

El crecimiento del sector pecuario está condicionado por la existencia de un mayor riesgo de enfermedades epidémicas. La creciente diseminación de nuevas enfermedades a partir de animales silvestres es consecuencia de transformaciones antrópicas a gran escala que posibilitan un contacto más frecuente y estrecho de la fauna silvestre con el ser humano y el ganado. Cada vez son más las epidemias del ganado que tienen que ver con la rápida transición de los sistemas pecuarios de un régimen de producción extensiva a otro de producción intensiva y con el paso de la dimensión local a la mundial de la circulación de animales y sus derivados a través de redes de cadenas de valor que presentan una endeble seguridad biológica. En los últimos dos decenios ha habido grandes epidemias que han afectado al ganado y tenido importantes consecuencias económicas. La pandemia de COVID-19 es un elocuente ejemplo de los devastadores efectos socioeconómicos que puede tener la extensión de un patógeno cuando no se detecta y controla en un momento lo bastante precoz del proceso de emergencia. Ello pone de relieve la importancia que revisten los Servicios Veterinarios para que toda la sociedad pueda reaccionar de forma integrada a la hora de combatir las enfermedades infecciosas de los animales. Dentro de los Servicios Veterinarios, conviene poner el acento en la prevención y la preparación. Para lograr este objetivo los autores señalan cuatro ámbitos que exigen una constante mejora: a) el desarrollo continuo de la capacidad del personal en materia de determinación de riesgos y análisis de cadenas de valor, ligado a la mejora de las políticas y la comunicación; b) la adecuada adaptación de los métodos de prevención y control en contextos de escasos recursos; c) una mejor cooperación multisectorial y transfronteriza, que permita poner en común recursos y competencias técnicas; y d) enfoques sistemáticos que hagan posible que los Servicios Veterinarios influyan en los procesos decisorios relativos al desarrollo del comercio, los mercados, las empresas, la salud pública y los medios de sustento a escala tanto nacional como regional.

Prevalence and genotyping of Echinococcus granulosus sensu lato from livestock in north-eastern Kenya.

Cystic echinococcosis (CE) is a zoonotic disease of cosmopolitan distribution and caused by the larval stage of the dog tapeworm, Echinococcus granulosus sensu lato (s.l.). CE occurs in the wider African continent and in Kenya, notably in the Maasailand and Turkana regions; however, recent studies demonstrate its presence in other parts of Kenya. This study determined the occurrence of CE in livestock (camels, goats, sheep and cattle) in Isiolo, Garissa and Wajir counties, and characterized the species of E. granulosus s.l. present. An abattoir survey was used to determine the presence of CE in various organs in livestock. Polymerase chain reaction-restriction fragment length polymorphism and sequencing of the mitochondrial NADH dehydrogenase subunit 1 gene was used for genotyping. A total of 1368 carcasses from 687 goats, 234 camels, 329 sheep and 118 cattle were inspected for the presence of hydatid cysts. The overall proportion of infections was 29.1% in camels, 14.4% in cattle, 9.9% in goats and 8.2% in sheep. The liver was the most infected organ, while only the lung of camels harboured fertile cysts. Of the 139 cysts genotyped, 111 (79.9%) belonged to Echinococcus canadensis (G6/7) and 20 (14.4%) to E. granulosus sensu stricto. One and two cysts were identified as Taenia saginata and unknown Taenia species, respectively. There was a significant association between county of origin and species of the animal with occurrence of CE. This study reports, for the first time, the characterization of Echinococcus species in livestock from Garissa and Wajir counties, and the current situation in Isiolo county. The fertility of cysts in camels and frequency of E. canadensis (G6/7) in all livestock species indicate that camels play an important role in the maintenance of CE in the north-eastern counties of Kenya.

Association between Rift Valley fever virus seroprevalences in livestock and humans and their respective intra-cluster correlation coefficients, Tana River County, Kenya.

We implemented a cross-sectional study in Tana River County, Kenya, a Rift Valley fever (RVF)-endemic area, to quantify the strength of association between RVF virus (RVFv) seroprevalences in livestock and humans, and their respective intra-cluster correlation coefficients (ICCs). The study involved 1932 livestock from 152 households and 552 humans from 170 households. Serum samples were collected and screened for anti-RVFv immunoglobulin G (IgG) antibodies using inhibition IgG enzyme-linked immunosorbent assay (ELISA). Data collected were analysed using generalised linear mixed effects models, with herd/household and village being fitted as random variables. The overall RVFv seroprevalences in livestock and humans were 25.41% (95% confidence interval (CI) 23.49-27.42%) and 21.20% (17.86-24.85%), respectively. The presence of at least one seropositive animal in a household was associated with an increased odds of exposure in people of 2.23 (95% CI 1.03-4.84). The ICCs associated with RVF virus seroprevalence in livestock were 0.30 (95% CI 0.19-0.44) and 0.22 (95% CI 0.12-0.38) within and between herds, respectively. These findings suggest that there is a greater variability of RVF virus exposure between than within herds. We discuss ways of using these ICC estimates in observational surveys for RVF in endemic areas and postulate that the design of the sentinel herd surveillance should consider patterns of RVF clustering to enhance its effectiveness as an early warning system for RVF epidemics.

Estimating the between-farm transmission rates for highly pathogenic avian influenza subtype H5N1 epidemics in Bangladesh between 2007 and 2013.

Highly Pathogenic Avian Influenza (HPAI) is classified by the World Organization for Animal Health as one of the notifiable diseases. Its occurrence is associated with severe socio-economic impacts and is also zoonotic. Bangladesh HPAI epidemic data for the period between 2007 and 2013 were obtained and split into epidemic waves based on the time lag between outbreaks. By assuming the number of newly infected farms to be binomially distributed, we fit a Generalized Linear Model to the data to estimate between-farm transmission rates (ß). These parameters are then used together with the calculated infectious periods to estimate the respective basic reproduction numbers (R0 ). The change in ß and R0 with time during the course of each epidemic wave was explored. Finally, sensitivity analyses of the effects of reducing the delay in detecting infection on a farm as well as extended infectiousness of a farm beyond the day of culling were assessed. The point estimates obtained for ß ranged from 0.08 (95% CI: 0.06-0.10) to 0.11 (95% CI: 0.08-0.20) per infectious farm per day while R0 ranged from 0.85 (95% CI: 0.77-1.02) to 0.96 (95% CI: 0.72-1.20). Sensitivity analyses reveal that the estimates are quite robust to changes in the assumptions about the day in reporting infection and extended infectiousness. In the analysis allowing for time-varying transmission parameters, the rising and declining phases observed in the epidemic data were synchronized with the moments when R0 was greater and less than one, respectively. From an epidemiological perspective, the consistency of these estimates and their magnitude (R0  ≈ 1) indicate that the effectiveness of the deployed control measures was largely invariant between epidemic waves and the trend of the time-varying R0 supports the hypothesis of sustained farm-to-farm transmission that is possibly initiated by a few unique introductions.

Inter-epidemic Rift Valley fever virus seroconversions in an irrigation scheme in Bura, south-east Kenya.

Rift Valley fever (RVF) is an acute mosquito-borne viral zoonosis whose outbreaks are often associated with prolonged rainfall and flooding, during which large numbers of vectors emerge. Recent studies into the inter-epidemic maintenance of RVF virus (RVFV) suggest that both vertical transmission in vectors and direct transmission between hosts act in combination with predisposing factors for persistence of the virus. A comparative longitudinal survey was carried out in Tana River County, Kenya, in irrigated, riverine and pastoral ecosystems from September 2014-June 2015. The objectives were to investigate the possibility of low-level RVFV transmission in these ecosystems during an inter-epidemic period (IEP), examine variations in RVFV seroprevalence in sheep and goats and determine the risk factors for transmission. Three hundred and sixteen small ruminants were selected and tested for immunoglobulin G antibodies against RVFV nucleoprotein using a competitive ELISA during six visits. Data on potential risk factors were also captured. Inter-epidemic RVFV transmission was evidenced by 15 seroconversions within the irrigated and riverine villages. The number of seroconversions was not significantly different (OR = 0.66, CI = 0.19-2.17, p = .59) between irrigated and riverine areas. No seroconversions were detected in the pastoral ecosystem. This study highlights the increased risk of inter-epidemic RVFV transmission posed by irrigation, through provision of necessary environmental conditions that enable vectors access to more breeding grounds, resting places and shade, which favour their breeding and survival.

Effects of climate change on the occurrence and distribution of livestock diseases.

The planet's mean air and ocean temperatures have been rising over the last century because of increasing greenhouse gas (GHG) emissions. These changes have substantial effects on the epidemiology of infectious diseases. We describe direct and indirect processes linking climate change and infectious diseases in livestock with reference to specific case studies. Some of the studies are used to show a positive association between temperature and expansion of the geographical ranges of arthropod vectors (e.g. Culicoides imicola, which transmits bluetongue virus) while others are used to illustrate an opposite trend (e.g. tsetse flies that transmit a range of trypanosome parasites in sub-Saharan Africa). We further describe a positive association between extreme events: droughts and El Niño/southern oscillation (ENSO) weather patterns and Rift Valley fever outbreaks in East Africa and some adaptation practices used to mitigate the impacts of climate change that may increase risk of exposure to infectious pathogens. We conclude by outlining mitigation and adaptation measures that can be used specifically in the livestock sector to minimize the impacts of climate change-associated livestock diseases.

Effects of Irrigation and Rainfall on the Population Dynamics of Rift Valley Fever and Other Arbovirus Mosquito Vectors in the Epidemic-Prone Tana River County, Kenya.

Rift Valley fever (RVF) is a mosquito-borne viral zoonosis that is found in most regions of sub-Saharan Africa, and it affects humans, livestock, and some wild ungulates. Outbreaks are precipitated by an abundance of mosquito vectors associated with heavy persistent rainfall with flooding. We determined the impact of flood-irrigation farming and the effect of environmental parameters on the ecology and densities of primary and secondary vectors of the RVF virus (RVFV) in an RVF-epidemic hotspot in the Tana River Basin, Kenya. Mosquito sampling was conducted in farms and villages (settlements) in an irrigated and a neighboring nonirrigated site (Murukani). Overall, a significantly higher number of mosquitoes were collected in farms in the irrigation scheme compared with villages in the same area (P < 0.001), or farms (P < 0.001), and villages (P = 0.03) in Murukani. In particular, key primary vectors of RVFV, Aedes mcintoshi Marks and Aedes ochraceous Theobald, were more prevalent in the farms compared with villages in the irrigation scheme (P = 0.001) both during the dry and the wet seasons. Similarly, there was a greater abundance of secondary vectors, particularly Culex univittatus Theobald and Culex pipiens (L.) in the irrigation scheme than in the Murukani area. Rainfall and humidity were positively correlated with mosquito densities, particularly the primary vectors. Adult floodwater mosquitoes and Mansonia spp. were collected indoors; immatures of Ae. mcintoshi and secondary vectors were collected in the irrigation drainage canals, whereas those of Ae. ochraceous and Aedes sudanensis Theobald were missing from these water bodies. In conclusion, irrigation in RVF endemic areas provides conducive resting and breeding conditions for vectors of RVFV and other endemic arboviruses.

An approach for the identification of exemplar sites for scaling up targeted field observations of benthic biogeochemistry in heterogeneous environments.

Continental shelf sediments are globally important for biogeochemical activity. Quantification of shelf-scale stocks and fluxes of carbon and nutrients requires the extrapolation of observations made at limited points in space and time. The procedure for selecting exemplar sites to form the basis of this up-scaling is discussed in relation to a UK-funded research programme investigating biogeochemistry in shelf seas. A three-step selection process is proposed in which (1) a target area representative of UK shelf sediment heterogeneity is selected, (2) the target area is assessed for spatial heterogeneity in sediment and habitat type, bed and water column structure and hydrodynamic forcing, and (3) study sites are selected within this target area encompassing the range of spatial heterogeneity required to address key scientific questions regarding shelf scale biogeochemistry, and minimise confounding variables. This led to the selection of four sites within the Celtic Sea that are significantly different in terms of their sediment, bed structure, and macrofaunal, meiofaunal and microbial community structures and diversity, but have minimal variations in water depth, tidal and wave magnitudes and directions, temperature and salinity. They form the basis of a research cruise programme of observation, sampling and experimentation encompassing the spring bloom cycle. Typical variation in key biogeochemical, sediment, biological and hydrodynamic parameters over a pre to post bloom period are presented, with a discussion of anthropogenic influences in the region. This methodology ensures the best likelihood of site-specific work being useful for up-scaling activities, increasing our understanding of benthic biogeochemistry at the UK-shelf scale.

Risk factors for rotavirus infection in pigs in Busia and Teso subcounties, Western Kenya.

We analysed data that were previously collected for molecular characterisation of rotavirus (RV) groups A and C in pigs from Teso and Busia subcounties in Kenya to determine risk factors for its infection. The data included records from 239 randomly selected piglets aged between 1 and 6 months raised in free range and backyard production systems. RV infection was confirmed by screening of fresh faecal samples by using reverse transcription polymerase chain reaction (RT-PCR); selected positive samples were subsequently sequenced and used for phylogenetic analysis. In this analysis, RV infection status was used as outcome variable, while the metadata collected at the time of sampling were used as predictors. A Bayesian hierarchical model which used integrated nested Laplace approximation (INLA) method was then fitted to the data. The model accounted for the spatial effect by using stochastic partial differential equations (SPDEs). Of the 239 samples screened, 206 were available for the analysis. Descriptive analyses showed that 27.7 % (57/206) of the samples were positive for rotaviruses groups A and C, 18.5 % were positive for group A rotaviruses, 5.3 % were positive for group C rotaviruses, while 3.9 % had co-infections from both groups of rotaviruses. The spatial effect was insignificant, and a simple (non-spatial) model showed that piglets (≤4 months) and those pigs kept in free range systems had higher risk of exposure to rotavirus infection as compared to older pigs (>4 months) and those tethered or housed, respectively. Intervention measures that will target these high-risk groups of pigs will be beneficial to farmers.

High resolution study of the spatial distributions of abyssal fishes by autonomous underwater vehicle.

On abyssal plains, demersal fish are believed to play an important role in transferring energy across the seafloor and between the pelagic and benthic realms. However, little is known about their spatial distributions, making it difficult to quantify their ecological significance. To address this, we employed an autonomous underwater vehicle to conduct an exceptionally large photographic survey of fish distributions on the Porcupine Abyssal Plain (NE Atlantic, 4850 m water depth) encompassing two spatial scales (1-10 km(2)) on and adjacent to a small abyssal hill (240 m elevation). The spatial distributions of the total fish fauna and that of the two dominant morphotypes (Coryphaenoides sp. 1 and C. profundicolus) appeared to be random, a result contrary to common expectation but consistent with previous predictions for these fishes. We estimated total fish density on the abyssal plain to be 723 individuals km(-2) (95% CI: 601-844). This estimate is higher, and likely more precise, than prior estimates from trawl catch and baited camera techniques (152 and 188 individuals km(-2) respectively). We detected no significant difference in fish density between abyssal hill and plain, nor did we detect any evidence for the existence of fish aggregations at any spatial scale assessed.

Antibody response and risk factors for seropositivity in backyard poultry following mass vaccination against highly pathogenic avian influenza and Newcastle disease in Indonesia.

A large-scale mass vaccination campaign was carried out in Java, Indonesia in an attempt to control outbreaks of highly pathogenic avian influenza (HPAI) in backyard flocks and commercial smallholder poultry. Sero-monitoring was conducted in mass vaccination and control areas to assess the proportion of the target population with antibodies against HPAI and Newcastle disease (ND). There were four rounds of vaccination, and samples were collected after each round resulting in a total of 27 293 samples. Sampling was performed irrespective of vaccination status. In the mass vaccination areas, 20-45% of poultry sampled had a positive titre to H5 after each round of vaccination, compared to 2-3% in the control group. In the HPAI + ND vaccination group, 12-25% of the population had positive ND titres, compared to 5-13% in the areas without ND vaccination. The level of seropositivity varied by district, age of the bird, and species (ducks vs. chickens).

Estimating the transmissibility of H5N1 and the effect of vaccination in Indonesia.

The spread of H5N1 avian influenza continues to pose an economic burden and a public health risk worldwide. Despite this, estimates of the transmissibility of infection exist in only a handful of settings and vary considerably. Using final size methods and flock-level infection data from a field trial of mass vaccination, we obtained the first estimates of the transmissibility of infection between and within flocks in Indonesia. We also found that outbreaks in areas designated as vaccination zones were less transmissible than in non-vaccination zones. However, this reduction is only comparable with a limited degree of protective vaccination coverage. Quantifying the overall effect of vaccination in these zones remains challenging. However, this result would appear to imply that, although the interventions applied in vaccination zones were not sufficient to completely prevent transmission in all areas, when outbreaks occur, they are less transmissible than those in areas where vaccination was not applied. This could be either a direct or an indirect effect of vaccination. Given the dynamism of small-scale poultry production in Indonesia, more regular vaccination may be required to ensure that infection is fully controlled in vaccination zones.

The effectiveness of preventative mass vaccination regimes against the incidence of highly pathogenic avian influenza on Java Island, Indonesia.

We conducted an operational research study involving backyard and semicommercial farms on Java Island, Indonesia, between April 2008 and September 2009 to evaluate the effectiveness of two preventive mass vaccination strategies against highly pathogenic avian influenza (HPAI). One regimen used Legok 2003 H5N1 vaccine, while the other used both Legok 2003 H5N1 and HB1 Newcastle disease (ND) vaccine. A total of 16 districts were involved in the study. The sample size was estimated using a formal power calculation technique that assumed a detectable effect of treatment as a 50% reduction in the baseline number of HPAI-compatible outbreaks. Within each district, candidate treatment blocks with village poultry populations ranging from 80 000 to 120 000 were created along subdistrict boundary lines. Subsequently, four of these blocks were randomly selected and assigned one treatment from a list that comprised control, vaccination against HPAI, vaccination against HPAI + ND. Four rounds of vaccination were administered at quarterly intervals beginning in July 2008. A vaccination campaign involved vaccinating 100 000 birds in a treatment block, followed by another 100 000 vaccinations 3 weeks later as a booster dose. Data on disease incidence and vaccination coverage were also collected at quarterly intervals using participatory epidemiological techniques. Compared with the unvaccinated (control) group, the incidence of HPAI-compatible events declined by 32% (P = 0.24) in the HPAI-vaccinated group and by 73% (P = 0.00) in the HPAI- and ND-vaccinated group. The effect of treatment did not vary with time or district. Similarly, an analysis of secondary data from the participatory disease and response (PDSR) database revealed that the incidence of HPAI declined by 12% in the HPAI-vaccinated group and by 24% in the HPAI + ND-vaccinated group. The results suggest that the HPAI + ND vaccination significantly reduced the incidence of HPAI-compatible events in mixed populations of semicommercial and backyard poultry.

Transmission rate and reproductive number of the H5N1 highly pathogenic avian influenza virus during the December 2005-July 2008 epidemic in Nigeria.

We quantified the between-village transmission rate, ß (the rate of transmission of H5N1 HPAI virus per effective contact), and the reproductive number, Re (the average number of outbreaks caused by one infectious village during its entire infectious period), of H5N1 highly pathogenic avian influenza (HPAI) virus in Nigeria using outbreak data collected between December 2005 and July 2008. We classified the outbreaks into two phases to assess the effectiveness of the control measures implemented. Phase 1 (December 2005-October 2006) represents the period when the Federal Government of Nigeria managed the HPAI surveillance and response measures, while Phase 2 (November 2006-July 2008) represents the time during which the Nigeria Avian Influenza Control and Human Pandemic Preparedness project (NAICP), funded by a World Bank credit of US$ 50 million, had taken over the management of most of the interventions. We used a total of 204 outbreaks from 176 villages that occurred in 78 local government areas of 25 states. The compartmental susceptible-infectious model was used as the analytical tool. Means and 95% percentile confidence intervals were obtained using bootstrapping techniques. The overall mean ß (assuming a duration of infectiousness, T, of 12 days) was 0.07/day (95% percentile confidence interval: 0.06-0.09). The first and second phases of the epidemic had comparable ß estimates of 0.06/day (0.04-0.09) and 0.08/day (0.06-0.10), respectively. The Re of the virus associated with these ß and T estimates was 0.9 (0.7-1.1); the first and second phases of the epidemic had Re of 0.84 (0.5-1.2) and 0.9 (0.6-1.2), respectively. We conclude that the intervention measures implemented in the second phase of the epidemic had comparable effects to those implemented during the first phase and that the Re of the epidemic was low, indicating that the Nigeria H5N1 HPAI epidemic was unstable.

Population attributable fractions of farm vector tick (Rhipicephalus appendiculatus) presence on Theileria parva infection seroprevalence under endemic instability.

The primary objective of this study was to assess the impact of Rhipicephalus appendiculatus tick presence (exposure variable) on Theileria parva infection seroprevalence (outcome variable) in a group of cattle belonging to a farm using population attributable fractions (PAF). The analyses were based on a representative sample of 80 traditional smallholder mixed farms. The farms were selected by first stratifying the population administratively and implementing a multistage random sampling in Mbeere district in Kenya. The PAFs were estimated using the stratified, Bruzzi, and sequential partitioned PAF approaches. A secondary objective was, thus, to evaluate the impact of the approaches on the PAF estimates. The stratified and Bruzzi approaches estimated proportion of T. parva infection cases directly attributable to the exposure after controlling for confounding by agro-ecological zone (AEZ). The sequential partitioned PAF approach estimated a PAF associated with exposure after adjusting for any effect that the AEZ may have had by influencing the prevalence of the exposure. All analyses were carried out at the farm level where a farm was classified as infested if the tick was found on cattle on a farm, and infected if at least one animal on a farm was positive for T. parva antibodies. Variance estimation for PAFs was implemented using 'delete-a-group' jackknife re-sampling method. The stratified PAF (26.7% [95% CI: 9.0%, 44.4%]) and Bruzzi PAF (26.4% [95% CI: 9.6%, 43.2%]) were consistent in estimating a relatively low impact of farm vector tick presence with a relatively high level of uncertainty. The partitioned PAF (15.5% [95% CI: 1.5%, 29.6%]) suggested that part of the impacts estimated using the stratified PAF and Bruzzi approaches was driven by AEZ effects. Overall, the results suggested that under endemic instability in Mbeere district, (1) presence of R. appendiculatus was not a good indicator of T. parva infection occurrence on a farm; (2) ecological variation could play a role in determining infection impacts. This study provides a preliminary basis for evaluating the potential value and utility of estimating PAFs for variables amenable to control in tick-borne diseases (TBDs) epidemiological studies.

Incidence of highly pathogenic avian influenza H5N1 in Nigeria, 2005-2008.

Outbreaks of highly pathogenic avian influenza (HPAI) H5N1 occurred in Nigeria between December 2005 and July 2008. We describe temporal and spatial characteristics of these outbreaks at State and Local Government Area (LGA) levels. A total of 25 of 37 States (67.6%; Exact 95% CI: 50.2-82.0%) and 81 of 774 LGAs (10.5%; Exact 95% CI: 8.4-12.8%) were affected by HPAI outbreaks over the period from 2005 to 2008. The incidence risk of HPAI outbreak occurrence at the State level was 5.6% (0.7-18.7%) for 2005, 50.0% (30.7-69.4%) for 2006, 54.5% (29.9-80.3%) for 2007 and 0% for 2008. Only very few LGAs experienced HPAI outbreaks within the affected States. The incidence risk of HPAI outbreak occurrence on a LGA level was 0.3% (0.0-0.9%) for 2005, 6.6% (4.9-8.6%) for 2006, 4.2% (2.9-6.0%) for 2007 and 0% for 2008. The mean period between farmers noticing HPAI outbreaks and reporting them to veterinary authorities, and between reporting HPAI outbreaks and the depopulation of infected premises, was for both 4.5 days; both periods also had medians of 1 day. We have estimated the spatially smoothed incidence risk for the whole outbreak period and identified the existence of a large corridor in the western part of Nigeria and a smaller corridor in south-eastern part, where the risk of HPAI occurrence was lower than in the rest of the country. The effect of HPAI control policies on the outbreaks patterns are discussed, as well as possible reasons why HPAI did not become endemic in Nigeria.

The 2006-2007 Rift Valley fever outbreak in Kenya: sources of early warning messages and response measures implemented by the Department of Veterinary Services.

The authors characterised sources of early warning messages about occurrences of Rift Valley fever (RVF) and examined the response measures that were used by the Department of Veterinary Services (DVS) to manage the 2006-2007 RVF outbreaks in Kenya. The study was conducted between November 2009 and March 2010 and it included national, provincial and district veterinary officers who were involved in the management of the outbreak. Structured questionnaires were used to collect the data. Although the majority of the respondents reported having limited capacity to implement response measures, they perceived that the measures implemented were effective. Vaccination, movement control and market closures were the main response measures implemented, particularly in districts that had cases in both livestock and humans. Vaccination, however, was implemented too late and the coverage achieved was too low to be effective. The authors suggest ways to improve the capacity of the DVS to respond to similar outbreaks in the future.

Integration of participatory approaches into surveillance systems.

Animal health surveillance is essential for protecting public health, enhancing access to international markets for animals and their products, and improving animal health, production and welfare. It is of vital importance for protecting and improving the livelihoods of diverse groups of livestock keepers and stakeholders in livestock value chains. Surveillance systems consist of sets of complementary components which generate information to inform risk assessment, decision-making and policy formulation for both national programmes and international trade. Participatory approaches have the potential to add value to surveillance systems by enhancing their performance, especially their sensitivity and timeliness, and encouraging the inclusion of marginalised groups. This paper summarises key considerations in the assessment and design of animal health surveillance and discusses how participatory approaches can be integrated into comprehensive surveillance systems, leading to a more effective overall outcome for both domestic and international purposes.