Julien Cappelle

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.

Predicting Hotspots for Influenza Virus Reassortment

TOC summary: Reassortment is most likely to occur in eastern China, central China, or the Nile Delta in Egypt.

Duck Migration and Past Influenza A (H5N1) Outbreak Areas

To the Editor: In 2005 and 2006, the highly pathogenic avian influenza (HPAI) virus subtype H5N1 rapidly spread from Asia through Europe, the Middle East, and Africa. Waterbirds are considered the natural reservoir of low pathogenic avian influenza viruses (1), but their potential role in the spread of HPAI (H5N1), along with legal and illegal poultry and wildlife trade (2), is yet to be clarified. The garganey (Anas querquedula) is the most numerous duck migrating between Eurasia and Africa: ≈2 million gather in the wetlands of Western Africa every northern winter (3). We report on a spatial correlation between the 2007 migration path of a garganey monitored through satellite telemetry and areas that had major HPAI (H5N1) outbreaks from 2005 through 2007. Seven garganeys were captured, sampled, and fitted with a 12-g satellite transmitter in northern Nigeria (Hadejia-Nguru Wetlands; 12°48′N; 10°44′E) in the period February 7–15, 2007. All cloacal and tracheal swabs tested negative for avian influenza virus by real-time reverse transcription–PCR analysis of the matrix gene. One second-year (>9-month-old) female garganey migrated from northern Nigeria to Russia in April–May 2007 (Appendix Figure), where she remained until the end of July. During this 6-week spring migration over the Sahara Desert, Mediterranean Sea, and Eastern Europe, this duck stopped at 3 main stopover sites in Crete, Turkey (Bosphorus region), and Romania (Danube River delta). The duck migrated back to the Danube delta in August, where it remained until November, when the signal was lost. Other garganeys we monitored stopped transmitting before initiating spring migration (n = 3) or remained in West Africa during spring and summer (n = 3), which suggests a stress linked to capture or constraint from the transmitter attachment. This transcontinental migration path connects several areas of past major HPAI (H5N1) outbreaks (Appendix Figure). The wintering area in Nigeria where this duck was caught and remained for 8 weeks before spring migration is located where a large number of outbreaks have occurred repeatedly since February 2006 (the closest being 30 km away). This bird reached its breeding ground in Russia near Moscow and stayed for 2 months in an area that had several outbreaks in backyard poultry in February 2007 (the closest being 30 km away). Finally, the Danube delta, used as a resting ground for 3 months in late summer and autumn, is also an area with recurring outbreaks since October 2005 in wild and domestic birds, with the most recent case reported in November 2007 (the closest being 10 km away). The initial spread of HPAI virus (H5N1) from Eurasia to Africa occurred in autumn and winter 2005–06. The migratory movements we observed during spring and summer in this study were not temporally correlated with any reported HPAI (H5N1) outbreak, either in sequence or period; hence, they should not be interpreted as evidence of the role of wild bird in expansions of the virus. During spring migration from Nigeria to Russia, the garganey stopped several days in wetlands situated close to areas of past outbreaks in the Danube delta (4 days at a distance of 1–4 km from October 2005 outbreaks) and Lake Kus, Turkey (8 days at a distance of 10–30 km from October 2005 outbreaks). The occurrence of past outbreaks indicates that the duck used wetlands favorable to HPAI virus (H5N1) transmission as stopover sites. The relatively long stopover periods enabled prolonged contact of migratory ducks with local domestic and wild bird populations or through shared water, thus prolonging the potential for virus transmission. Considering the persistence of infectivity of HPAI virus (H5N1) in aquatic habitats (4), the number of migratory ducks congregating at stopover sites from various geographic origins and destinations, and the asynchronous timing of the arrival and departure of migratory ducks (5), we believe that these sites may provide locations for disease transmission and possible spread upon movement of wild birds. The satellite-fitted female garganey covered distances between stopover sites of >2,000 km in <2 days, traveling at an estimated speed of 60 km/h. This large-scale movement in a short period, coupled with experimental exposure trials demonstrating viral shedding of up to 4 days in ducks with no clinical signs of infection (6), is consistent with potential viral transmission over great distances. These facts illustrate how a pathogen such as HPAI virus (H5N1) can potentially be transported rapidly by migratory birds across continents. However, the physiologic impact of an HPAI (H5N1) infection on the ability of birds to migrate long distances is still unknown (7) and to date, most empirical evidence suggests that wild birds have only moved short distances (a few hundred kilometers) likely carrying HPAI virus (H5N1) (8). Despite extensive global wildlife surveillance efforts and with the exception of a few reported cases of HPAI (H5N1) infection in apparently healthy wild ducks (9,10), evidence of wild bird involvement in the spread of HPAI virus (H5N1) over long distances is still lacking.

Estimating the burden of Japanese encephalitis virus and other encephalitides in countries of the mekong region.

Diverse aetiologies of viral and bacterial encephalitis are widely recognized as significant yet neglected public health issues in the Mekong region. A robust analysis of the corresponding health burden is lacking. We retrieved 75 articles on encephalitis in the region published in English or in French from 1965 through 2011. Review of available data demonstrated that they are sparse and often derived from hospital-based studies with significant recruitment bias. Almost half (35 of 75) of articles were on Japanese encephalitis virus (JEV) alone or associated with dengue. In the Western Pacific region the WHO reported 30,000–50,000 annual JEV cases (15,000 deaths) between 1966 and 1996 and 4,633 cases (200 deaths) in 2008, a decline likely related to the introduction of JEV vaccination in China, Vietnam, or Thailand since the 1980s. Data on dengue, scrub typhus and rabies encephalitis, among other aetiologies, are also reviewed and discussed. Countries of the Mekong region are undergoing profound demographic, economic and ecological change. As the epidemiological aspects of Japanese encephalitis (JE) are transformed by vaccination in some countries, highly integrated expert collaborative research and objective data are needed to identify and prioritize the human health, animal health and economic burden due to JE and other pathogens associated with encephalitides.

Investigating Avian Influenza Infection Hotspots in Old-World Shorebirds

Heterogeneity in the transmission rates of pathogens across hosts or environments may produce disease hotspots, which are defined as specific sites, times or species associations in which the infection rate is consistently elevated. Hotspots for avian influenza virus (AIV) in wild birds are largely unstudied and poorly understood. A striking feature is the existence of a unique but consistent AIV hotspot in shorebirds (Charadriiformes) associated with a single species at a specific location and time (ruddy turnstone Arenaria interpres at Delaware Bay, USA, in May). This unique case, though a valuable reference, limits our capacity to explore and understand the general properties of AIV hotspots in shorebirds. Unfortunately, relatively few shorebirds have been sampled outside Delaware Bay and they belong to only a few shorebird families; there also has been a lack of consistent oropharyngeal sampling as a complement to cloacal sampling. In this study we looked for AIV hotspots associated with other shorebird species and/or with some of the larger congregation sites of shorebirds in the old world. We assembled and analysed a regionally extensive dataset of AIV prevalence from 69 shorebird species sampled in 25 countries across Africa and Western Eurasia. Despite this diverse and extensive coverage we did not detect any new shorebird AIV hotspots. Neither large shorebird congregation sites nor the ruddy turnstone were consistently associated with AIV hotspots. We did, however, find a low but widespread circulation of AIV in shorebirds that contrast with the absence of AIV previously reported in shorebirds in Europe. A very high AIV antibody prevalence coupled to a low infection rate was found in both first-year and adult birds of two migratory sandpiper species, suggesting the potential existence of an AIV hotspot along their migratory flyway that is yet to be discovered.

New avian paramyxoviruses Type I strains identified in Africa provide new outcomes for phylogeny reconstruction and genotype classification

Newcastle disease (ND) is one of the most lethal diseases of poultry worldwide. It is caused by an avian paramyxovirus 1 that has high genomic diversity. In the framework of an international surveillance program launched in 2007, several thousand samples from domestic and wild birds in Africa were collected and analyzed. ND viruses (NDV) were detected and isolated in apparently healthy fowls and wild birds. However, two thirds of the isolates collected in this study were classified as virulent strains of NDV based on the molecular analysis of the fusion protein and experimental in vivo challenges with two representative isolates. Phylogenetic analysis based on the F and HN genes showed that isolates recovered from poultry in Mali and Ethiopia form new groups, herein proposed as genotypes XIV and sub-genotype VIf with reference to the new nomenclature described by Diel’s group. In Madagascar, the circulation of NDV strains of genotype XI, originally reported elsewhere, is also confirmed. Full genome sequencing of five African isolates was generated and an extensive phylogeny reconstruction was carried out based on the nucleotide sequences. The evolutionary distances between groups and the specific amino acid signatures of each cluster allowed us to refine the genotype nomenclature.

Bridge hosts, a missing link for disease ecology in multi-host systems

In ecology, the grouping of species into functional groups has played a valuable role in simplifying ecological complexity. In epidemiology, further clarifications of epidemiological functions are needed: while host roles may be defined, they are often used loosely, partly because of a lack of clarity on the relationships between a host’s function and its epidemiological role. Here we focus on the definition of bridge hosts and their epidemiological consequences. Bridge hosts provide a link through which pathogens can be transmitted from maintenance host populations or communities to receptive populations that people want to protect (i.e., target hosts). A bridge host should (1) be competent for the pathogen or able to mechanically transmit it; and (2) come into direct contact or share habitat with both maintenance and target populations. Demonstration of bridging requires an operational framework that integrates ecological and epidemiological approaches. We illustrate this framework using the example of the transmission of Avian Influenza Viruses across wild bird/poultry interfaces in Africa and discuss a range of other examples that demonstrate the usefulness of our definition for other multi-host systems. Bridge hosts can be particularly important for understanding and managing infectious disease dynamics in multi-host systems at wildlife/domestic/human interfaces, including emerging infections.

Risks of avian influenza transmission in areas of intensive free-ranging duck production with wild waterfowl

For decades, southern China has been considered to be an important source for emerging influenza viruses since key hosts live together in high densities in areas with intensive agriculture. However, the underlying conditions of emergence and spread of avian influenza viruses (AIV) have not been studied in detail, particularly the complex spatiotemporal interplay of viral transmission between wild and domestic ducks, two major actors of AIV epidemiology. In this synthesis, we examine the risks of avian influenza spread in Poyang Lake, an area of intensive free-ranging duck production and large numbers of wild waterfowl. Our synthesis shows that farming of free-grazing domestic ducks is intensive in this area and synchronized with wild duck migration. The presence of juvenile domestic ducks in harvested paddy fields prior to the arrival and departure of migrant ducks in the same fields may amplify the risk of AIV circulation and facilitate the transmission between wild and domestic populations. We provide evidence associating wild ducks migration with the spread of H5N1 in the spring of 2008 from southern China to South Korea, Russia, and Japan, supported by documented wild duck movements and phylogenetic analyses of highly pathogenic avian influenza H5N1 sequences. We suggest that prevention measures based on a modification of agricultural practices may be implemented in these areas to reduce the intensity of AIV transmission between wild and domestic ducks. This would require involving all local stakeholders to discuss feasible and acceptable solutions.

Value of Routine Dengue Diagnostic Tests in Urine and Saliva Specimens.

Background Dengue laboratory diagnosis is essentially based on detection of the virus, its components or antibodies directed against the virus in blood samples. Blood, however, may be difficult to draw in some patients, especially in children, and sampling during outbreak investigations or epidemiological studies may face logistical challenges or limited compliance to invasive procedures from subjects. The aim of this study was to assess the possibility of using saliva and urine samples instead of blood for dengue diagnosis. Methodology/Principal Findings Serial plasma, urine and saliva samples were collected at several time-points between the day of admission to hospital until three months after the onset of fever in children with confirmed dengue disease. Quantitative RT-PCR, NS1 antigen capture and ELISA serology for anti-DENV antibody (IgG, IgM and IgA) detection were performed in parallel on the three body fluids. RT-PCR and NS1 tests demonstrated an overall sensitivity of 85.4%/63.4%, 41.6%/14.5% and 39%/28.3%, in plasma, urine and saliva specimens, respectively. When urine and saliva samples were collected at the same time-points and tested concurrently, the diagnostic sensitivity of RNA and NS1 detection assays was 69.1% and 34.4%, respectively. IgG/IgA detection assays had an overall sensitivity of 54.4%/37.4%, 38.5%/26.8% and 52.9%/28.6% in plasma, urine and saliva specimens, respectively. IgM were detected in 38.1% and 36% of the plasma and saliva samples but never in urine. Conclusions Although the performances of the different diagnostic methods were not as good in saliva and urine as in plasma specimens, the results obtained by qRT-PCR and by anti-DENV antibody ELISA could well justify the use of these two body fluids to detect dengue infection in situations when the collection of blood specimens is not possible.

A meta-analysis of observational epidemiological studies of Newcastle disease in African agro-systems, 1980-2009

Newcastle disease (ND) is one of the most important and widespread avian pests. In Africa, backyard poultry production systems are an important source of protein and cash for poor rural livelihoods. ND mortality in these production systems is important and seriously disrupts benefits derived from it. This study undertook an African continental approach of ND epidemiology in backyard poultry. After a systematic literature review of studies published from 1980 to 2009, a meta-analysis of spatio-temporal patterns of serological prevalence and outbreak occurrence was performed. Average ND serological prevalence was estimated at 0·67 [95% confidence interval (CI) 0·58-0·75] in regions characterized by humid ecosystems, high human and poultry densities and low altitudes; 0·36 (95% CI 0·30-0·41) in dry ecosystems at intermediate altitude where human and poultry densities are low and 0·27 (95% CI 0·19-0·38) in mountain ecosystems where human and poultry densities are intermediate. In terms of seasonality, ND outbreaks occur mostly during the dry seasons in Africa, when environmental conditions are likely to be harshest for backyard poultry. In addition, a phylogeographical analysis revealed the regionalization of ND virus strains, their potential to evolve towards a higher pathogenicity from the local viral pool and suggests a risk for vaccine strains to provide new wild strains. These results present for the first time a continent-wide approach to ND epidemiology in Africa. More emphasis is needed for ND management and control in rural African poultry production systems.