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Abstract Background Leptospirosis is a zoonotic disease. It is particularly prevalent in tropical countries and has major consequences for human and animal health. In Benin, the disease's epidemiology remains poorly understood, especially in livestock, for which data are lacking. Objectives To characterise Leptospira seroprevalence and locally circulating serogroups in livestock from Cotonou and to estimate the prevalence of Leptospira renal carriage in cattle. Methods We conducted a cross‐sectional study in February 2020 during which livestock were sampled at an abattoir and in an impoverished city district. We analysed blood samples from 279 livestock animals (i.e. cattle, sheep, goats and pigs) using the microscopic agglutination test. Additionally, samples of renal tissue from 100 cattle underwent 16s rRNA (rrs) real‐time PCR analysis. Results For the 131 cattle, 85 sheep, and 50 goats tested, seroprevalence was 18% (95% confidence interval [CI] [12%, 26%]), 9% (95% CI [4%, 17%] and 2% (95% CI [0%, 9%]), respectively, and most of the seropositive animals were associated with 1:100 titres. All 13 pigs were seronegative. Leptospira DNA was found in the renal tissue of 10% (95% CI [5%, 18%]) of the cattle tested (n = 100). Leptospira borgpetersenii was the main species present (n = 7), but Leptospira interrogans (n = 2) and Leptospira kirschneri (n = 1) were also detected. Various serogroups (Canicola, Grippotyphosa, Sejroe, Icterohaemorrhagiae, Pomona, Pyrogenes, Australis and Autumnalis) were detected using microscopic agglutination test without a clear predominance of any of them. Conclusions These results suggest that abattoir workers and people living in close contact with livestock in poor urban areas are exposed to the risk of Leptospira infection.

Abstract Studying wildlife space use in human‐modified environments contributes to characterize wildlife‐human interactions to assess potential risks of zoonotic‐pathogens transmission, and to pinpoint conservation issues. In central African rainforests with human dwelling and activities, we conducted a telemetry study on a group of males of Hypsignathus monstrosus, a lek‐mating fruit bat identified as a potential maintenance host for Ebola virus. During a lekking season in 2020, we investigated the foraging‐habitat selection and the individual nighttime space use during both mating and foraging activities close to villages and their surrounding agricultural landscape. At night, marked individuals strongly selected agricultural lands and more generally areas near watercourses to forage, where they spent more time compared to forest ones. Furthermore, the probability and duration of the presence of bats in the lek during nighttime decreased with the distance to their roost site but remained relatively high within a 10 km radius. Individuals adjusted foraging behaviors according to mating activity by reducing both the overall time spent in foraging areas and the number of forest areas used to forage when they spent more time in the lek. Finally, the probability of a bat revisiting a foraging area in the following 48 hours increased with the previous time spent in that foraging area. These behaviors occurring close to or in human‐modified habitats can trigger direct and indirect bat‐human contacts, which could thus facilitate pathogen transmission such as Ebola virus.

Abstract The role of commensal birds in the epidemiology of pathogens in poultry farms remains unclear. Our study aimed to identify potential key species for interactions with domestic ducks on one free-range duck farm in southwest France. Methods combined direct individual observations on duck outdoor foraging areas, network analysis, and general linear mixed models of abundances. Results showed a wide diversity of wild bird species visiting foraging areas, heavily dominated in frequency by White wagtails (Motacilla alba) and Sparrows (Passer domesticus and Passer montanus). These also were the only species seen entering duck premises or perching on drinkers in the presence of ducks. Moreover, White wagtails were the species most frequently observed on the ground and in close proximity to ducks. Network analysis suggested the role of White wagtails and Sparrows in linking ducks to other wild birds on the farm. The abundance of White wagtails was positively associated with open vegetation, with the presence of ducks and particularly in the afternoon, while the abundance of Sparrows was positively associated only with the fall-winter season. By precisely characterising interactions, the study was able to identify few wild bird species which should be prioritized in infectious investigations at the interface with poultry.

⁎Presenting authorEmerging infectious diseases have been causing outbreaks in humans for centuries and most infectious diseases originate in animals. Re-emerging zoonotic pathogens are rapidly increasing in prevalence or geographic range and causing a significant and growing threat to global health. The present work provides an insight of zoonotic viruses risk at human-bat/rodent interfaces in Cambodia.We conducted studies to investigate the circulation of zoonotic viruses and the risk of exposure in human living at the interfaces with bats and rodents. Rodent's samples were collected in rural and urban areas of Cambodia. Organs were tested for Hantavirus, Orthohepevirus species C and Arenavirus. Bat's samples were collected in Steung Treng for Sarbecovirus and in Battambang and Kandal for Nipah virus detection. People working/living at the human-animal interfaces were screened for IgG antibodies.In rodents (750), hantavirus was detected in 3.3% rodents from urban areas only. Seoul orthohantavirus was the most predominant virus followed by Thottapalayam virus. HEV-C was detected only in rodents from urban settings (1.8%). Arenavirus was detected in both rural (6.8%) and urban (2.5%) areas. In humans (788), the seroprevalence of IgG antibodies against hantavirus, HEV-A and Arenavirus was 10.0%, 24% and 23.4% respectively.NiV was detected in flying fox's urines collected between 2013-2016 in Kandal (0.63%) and in Battambang (1.03%). Blood samples collected in both provinces were negative for NiV antibodies.SARS-CoV-2 related virus was detected in Rhinolphus shameli in Steung Treng in 2010, 2020 and 2021. Blood samples from people living at the vicinity of positive bats were positive for antibodies against CoV (7.7%), but no specific neutralizing SARS-CoV2 antibodies were detected.Our studies provided insight of the risk of zoonoses in Cambodia and highlighted the importance of zoonotic surveillance and further One Health effort to prevent, detect, and respond to future cross-species transmission.

Abstract Background Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira and is responsible for significant economic porcine livestock losses. Knowledge of Leptospira serogroups and their distributions is important for evaluation of the relevance of leptospirosis management measures, including use of the prophylactic vaccine that was recently made available in France. A retrospective study was conducted to determine the relationships between different circulating Leptospira serogroups. Pigs from across France presenting clinical signs suggestive of leptospirosis were tested with the microagglutination test (MAT) between 2011 and 2017. We used weighted averages to determine serogroup distributions according to MAT results and considering cross-reactions. Results A total of 19,395 pig sera, mostly from Brittany, were tested, and 22.7% were found to be positive for at least one Leptospira serogroup. Analysis of the 4,346 seropositive results for which the putative infective serogroup could be defined, revealed that two out of ten serogroups were much more frequent than the others: Australis (48.5%) and Icterohaemorrhagiae (38.2%). Other serogroups, including Autumnalis, Panama, Ballum, Tarassovi, Sejroe, Grippotyphosa, Bataviae, and Pomona, were less common. Conclusions Although diagnostic laboratory data cannot be extrapolated to infer the distribution of Leptospira serogroups at the nationwide scale in France, the analysis of such data can provide an overview of the relationship between circulating Leptospira serogroups in space and time. During the last decade, protection against the serogroups Australis and Icterohaemorrhagiae would have prevented most of the clinical porcine leptospirosis cases in the large number of farms that we studied. In the future, epidemiological information related to circulating Leptospira serogroups should be extracted from data with a standardized approach for use in nationwide or international surveillance and prophylactic strategy support.

Abstract Leptospirosis is a globally important zoonotic disease. The disease is particularly important in tropical and subtropical countries. Infections in humans can be caused by exposure to infected animals or contaminated soil or water, which are suitable for Leptospira. To explore the cluster area, the Global Moran’s I index was calculated for incidences per 100,000 population at the province level during 2012–2018, using the monthly and annual data. The high-risk and low-risk provinces were identified using the local indicators of spatial association (LISA). The risk factors for leptospirosis were evaluated using a generalized linear mixed model (GLMM) with zero-inflation. We also added spatial and temporal correlation terms to take into account the spatial and temporal structures. The Global Moran’s I index showed significant positive values. It did not demonstrate a random distribution throughout the period of study. The high-risk provinces were almost all in the lower north-east and south parts of Thailand. For yearly reported cases, the significant risk factors from the final best-fitted model were population density, elevation, and primary rice crop arable areas. Interestingly, our study showed that leptospirosis cases were associated with large areas of rice production but were less prevalent in areas of high rice productivity. For monthly reported cases, the model using temperature range was found to be a better fit than using percentage of flooded area. The significant risk factors from the model using temperature range were temporal correlation, average soil moisture, normalized difference vegetation index, and temperature range. Temperature range, which has strongly negative correlation to percentage of flooded area was a significant risk factor for monthly data. Flood exposure controls should be used to reduce the risk of leptospirosis infection. These results could be used to develop a leptospirosis warning system to support public health organizations in Thailand.

With over 1,400 species worldwide, bats represent the second largest order of mammals after rodents, and are known to host major zoonotic pathogens. Here, we estimate the presence of pathogens in autochthonous bat populations. First, we set out to check our samples for PCR amplification efficiency by assessing the occurrence of inhibited PCR reactions from different types of bat samples with amplifying the housekeeping gene β-actin. Second, we investigated the presence of five targeted pathogens in a French bat population using PCR. We targeted viral RNA of Canine distemper virus, Alphacoronavirus, Lyssavirus, Rotavirus and bacterial Leptospira DNA. To do so, we screened for these viruses in bat faecal samples as well as in oropharyngeal swab samples. The presence of Leptospira was assessed in urine, kidney, lung and faecal samples. Results showed a frequency of inhibited reactions ranging from 5 to 60% of samples, varying according to the sample itself and also suspected to vary according to sampling method and the storage buffer solution used, demonstrating the importance of the sampling and storage on the probability of obtaining negative PCR results. For pathogen assessment, rotavirus and alphacoronavirus RNA were detected in Myotis myotis, Myotis daubentonii, Myotis emarginatus and Rhinolophus ferrumequinum bats. Rotaviruses were also detected in Barbastella barbastellus. The presence of alphacoronavirus also varied seasonally, with higher frequencies in late summer and October, suggesting that juveniles potentially play an important role in the dynamics of these viruses. Leptospira DNA was detected in M. myotis and M. daubentonii colonies. The 16S rRNA sequences obtained from Leptospira positive samples showed 100% genetic identity with L. borgpetersenii. Neither canine distemper virus nor lyssavirus RNA were detected in any of the tested samples. This study is the first to show the presence of Leptospira in autochthonous French bats in addition to coronavirus and rotavirus RNA previously reported in European autochthonous bats.

Abstract This socio-anthropological study investigates the relations between humans and rodents in an area adjacent to the Limpopo National Park in Mozambique. Designed as part of the larger researcher on mammarenaviruses, it explores the social dimensions of the rodent-human interface, considering its spatial and temporal variability. Its results contribute to our understanding of the socio-ecological context in which new pathogens or new routes of pathogen transmission could arise and potentially spread diseases. A vulnerability-based approach was used to assess human exposure, sensibility and capacity to adapt to rodents. This study revealed: (i) Local knowledge of the dynamic of rodent populations over the last few decades, with new invasive rodents displacing native species; (ii) the social-ecological factors thought to be behind this invasion: climate change, new infrastructure (e.g., construction of a dam), new agricultural practices (e.g., cultivation of sunflowers) and policies (human resettlement); (iii) the significant impact associated with new invasive rodents (e.g., crop losses, damage to belongings), the limited capacity for individual and collective interventions to mitigate damage, and the little concern shown for rodent-related diseases; (iv) women and girls’ high vulnerability to potential rodent-borne diseases due to frequent direct and indirect contact with rodents in the domestic space; and (v) the added-value of using a vulnerability-based methodology, over the more commonly used Knowledge-Attitudes-Practices (KAP) methodology, to map the structural factors shaping the human-rodent interface and its dynamic. Our findings suggest that the vulnerability-based approach could offer an opportunity to better respond to the One Health ambition by integrating social dimensions of health and grasping the complexity of the social and material context in which new pathogens could emerge and spread. One Health Statement The present socio-anthropological study of the human-rodent interface comes in complement to a previous eco-epidemiological survey focusing on the rodent-virus interface. It explores the cultural and social dimensions of the interactions between rodent-human, considering spatial and temporal variability. In doing so, it contributes to the understanding of the socio-ecological dynamic, in which new viral transmission can occur and disease spread. It exemplifies, based on local knowledge, how socio-ecological changes can create new routes for the emerging virus and highlights the vulnerability of the exposed human population to address the potential related health risks. This multidisciplinary and dynamic approach of how humans and rodents interact, and how these interactions are shaped by their changing environment is a contribution to a systemic approach to health, in line with the One health paradigm.

Abstract Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus. Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46–7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.

Summary: Background: Encephalitis is a worldwide public health issue, with a substantially high burden among children in southeast Asia. We aimed to determine the causes of encephalitis in children admitted to hospitals across the Greater Mekong region by implementing a comprehensive state-of-the-art diagnostic procedure harmonised across all centres, and identifying clinical characteristics related to patients’ conditions. Methods: In this multicentre, observational, prospective study of childhood encephalitis, four referral hospitals in Cambodia, Vietnam, Laos, and Myanmar recruited children (aged 28 days to 16 years) who presented with altered mental status lasting more than 24 h and two of the following minor criteria: fever (within the 72 h before or after presentation), one or more generalised or partial seizures (excluding febrile seizures), a new-onset focal neurological deficit, cerebrospinal fluid (CSF) white blood cell count of 5 per mL or higher, or brain imaging (CT or MRI) suggestive of lesions of encephalitis. Comprehensive diagnostic procedures were harmonised across all centres, with first-line testing was done on samples taken at inclusion and results delivered within 24 h of inclusion for main treatable causes of disease and second-line testing was done thereafter for mostly non-treatable causes. An independent expert medical panel reviewed the charts and attribution of causes of all the included children. Using multivariate analyses, we assessed risk factors associated with unfavourable outcomes (ie, severe neurological sequelae and death) at discharge using data from baseline and day 2 after inclusion. This study is registered with ClinicalTrials.gov, NCT04089436, and is now complete. Findings: Between July 28, 2014, and Dec 31, 2017, 664 children with encephalitis were enrolled. Median age was 4·3 years (1·8–8·8), 295 (44%) children were female, and 369 (56%) were male. A confirmed or probable cause of encephalitis was identified in 425 (64%) patients: 216 (33%) of 664 cases were due to Japanese encephalitis virus, 27 (4%) were due to dengue virus, 26 (4%) were due to influenza virus, 24 (4%) were due to herpes simplex virus 1, 18 (3%) were due to Mycobacterium tuberculosis, 17 (3%) were due to Streptococcus pneumoniae, 17 (3%) were due to enterovirus A71, 74 (9%) were due to other pathogens, and six (1%) were due to autoimmune encephalitis. Diagnosis was made within 24 h of admission to hospital for 83 (13%) of 664 children. 119 (18%) children had treatable conditions and 276 (42%) had conditions that could have been preventable by vaccination. At time of discharge, 153 (23%) of 664 children had severe neurological sequelae and 83 (13%) had died. In multivariate analyses, risk factors for unfavourable outcome were diagnosis of M tuberculosis infection upon admission (odds ratio 3·23 [95% CI 1·04–10·03]), coma on day 2 (2·90 [1·78–4·72]), supplementary oxygen requirement (1·89 [1·25–2·86]), and more than 1 week duration between symptom onset and admission to hospital (3·03 [1·68–5·48]). At 1 year after inclusion, of 432 children who were discharged alive from hospital with follow-up data, 24 (5%) had died, 129 (30%) had neurological sequelae, and 279 (65%) had completely recovered. Interpretation: In southeast Asia, most causes of childhood encephalitis are either preventable or treatable, with Japanese encephalitis virus being the most common cause. We provide crucial information that could guide public health policy to improve diagnostic, vaccination, and early therapeutic guidelines on childhood encephalitis in the Greater Mekong region. Funding: Institut Pasteur, Institut Pasteur International Network, Fondation Merieux, Aviesan Sud, INSERM, Wellcome Trust, Institut de Recherche pour le Développement (IRD), and Fondation Total.

Abstract Background Improved understanding of the foraging ecology of bats in the face of ongoing habitat loss and modification worldwide is essential to their conservation and maintaining the substantial ecosystem services they provide. It is also fundamental to assessing potential transmission risks of zoonotic pathogens in human-wildlife interfaces. We evaluated the influence of environmental and behavioral variables on the foraging patterns of Pteropus lylei (a reservoir of Nipah virus) in a heterogeneous landscape in Cambodia. Methods We employed an approach based on animal-movement modeling, which comprised a path-segmentation method (hidden Markov model) to identify individual foraging-behavior sequences in GPS data generated by eight P. lylei. We characterized foraging localities, foraging activity, and probability of returning to a given foraging locality over consecutive nights. Generalized linear mixed models were also applied to assess the influence of several variables including proxies for energetic costs and quality of foraging areas. Results Bats performed few foraging bouts (area-restricted searches) during a given night, mainly in residential areas, and the duration of these decreased during the night. The probability of a bat revisiting a given foraging area within 48 h varied according to the duration previously spent there, its distance to the roost site, and the corresponding habitat type. We interpret these fine-scale patterns in relation to global habitat quality (including food-resource quality and predictability), habitat-familiarity and experience of each individual. Conclusions Our study provides evidence that heterogeneous human-made environments may promote complex patterns of foraging-behavior and short-term re-visitation in fruit bat species that occur in such landscapes. This highlights the need for similarly detailed studies to understand the processes that maintain biodiversity in these environments and assess the potential for pathogen transmission in human-wildlife interfaces.

With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.

The unexpected Ebola virus outbreak in West Africa in 2014 involving the Zaire ebolavirus made clear that other regions outside Central Africa, its previously documented niche, were at risk of future epidemics. The complex transmission cycle and a lack of epidemiological data make mapping areas at risk of the disease challenging. We used a Geographic Information System-based multicriteria evaluation (GIS-MCE), a knowledge-based approach, to identify areas suitable for Ebola virus spillover to humans in regions of Guinea, Congo and Gabon where Ebola viruses already emerged. We identified environmental, climatic and anthropogenic risk factors and potential hosts from a literature review. Geographical data layers, representing risk factors, were combined to produce suitability maps of Ebola virus spillover at the landscape scale. Our maps show high spatial and temporal variability in the suitability for Ebola virus spillover at a fine regional scale. Reported spillover events fell in areas of intermediate to high suitability in our maps, and a sensitivity analysis showed that the maps produced were robust. There are still important gaps in our knowledge about what factors are associated with the risk of Ebola virus spillover. As more information becomes available, maps produced using the GIS-MCE approach can be easily updated to improve surveillance and the prevention of future outbreaks.

Background: Studies have linked bats to outbreaks of viral diseases in human populations such as SARS-CoV-1 and MERS-CoV and the ongoing SARS-CoV-2 pandemic. Methods: We carried out a longitudinal survey from August 2020 to July 2021 at two sites in Zimbabwe with bat–human interactions: Magweto cave and Chirundu farm. A total of 1732 and 1866 individual bat fecal samples were collected, respectively. Coronaviruses and bat species were amplified using PCR systems. Results: Analysis of the coronavirus sequences revealed a high genetic diversity, and we identified different sub-viral groups in the Alphacoronavirus and Betacoronavirus genus. The established sub-viral groups fell within the described Alphacoronavirus sub-genera: Decacovirus, Duvinacovirus, Rhinacovirus, Setracovirus and Minunacovirus and for Betacoronavirus sub-genera: Sarbecoviruses, Merbecovirus and Hibecovirus. Our results showed an overall proportion for CoV positive PCR tests of 23.7% at Chirundu site and 16.5% and 38.9% at Magweto site for insectivorous bats and Macronycteris gigas, respectively. Conclusions: The higher risk of bat coronavirus exposure for humans was found in December to March in relation to higher viral shedding peaks of coronaviruses in the parturition, lactation and weaning months of the bat populations at both sites. We also highlight the need to further document viral infectious risk in human/domestic animal populations surrounding bat habitats in Zimbabwe.

The ecology of ebolaviruses is still poorly understood and the role of bats in outbreaks needs to be further clarified. Straw-colored fruit bats (Eidolon helvum) are the most common fruit bats in Africa and antibodies to ebolaviruses have been documented in this species. Between December 2018 and November 2019, samples were collected at approximately monthly intervals in roosting and feeding sites from 820 bats from an Eidolon helvum colony. Dried blood spots (DBS) were tested for antibodies to Zaire, Sudan, and Bundibugyo ebolaviruses. The proportion of samples reactive with GP antigens increased significantly with age from 0–9/220 (0–4.1%) in juveniles to 26–158/225 (11.6–70.2%) in immature adults and 10–225/372 (2.7–60.5%) in adult bats. Antibody responses were lower in lactating females. Viral RNA was not detected in 456 swab samples collected from 152 juvenile and 214 immature adult bats. Overall, our study shows that antibody levels increase in young bats suggesting that seroconversion to Ebola or related viruses occurs in older juvenile and immature adult bats. Multiple year monitoring would be needed to confirm this trend. Knowledge of the periods of the year with the highest risk of Ebolavirus circulation can guide the implementation of strategies to mitigate spill-over events.

BACKGROUND:Central nervous system (CNS) infections are important contributors to morbidity and mortality and the causative agents for ~50% patients are never identified. The causative agents of some CNS infections have distinct spatial and temporal patterns. METHODOLOGY/PRINCIPAL FINDINGS:Here we present the results of a spatial epidemiological and ecological analysis of CNS infections in Lao PDR (2003-2011). The data came from hospitalizations for suspected CNS infection at Mahosot Hospital in Vientiane. Out of 1,065 patients, 450 were assigned a confirmed diagnosis. While many communities in Lao PDR are in rural and remote locations, most patients in these data came from villages along major roads. Japanese encephalitis virus ((JEV); n = 94) and Cryptococcus spp. (n = 70) were the most common infections. JEV infections peaked in the rainy season and JEV patients came from villages with higher surface flooding during the same month as admission. JEV infections were spatially dispersed throughout rural areas and were most common in children. Cryptococcus spp. infections clustered near Vientiane (an urban area) and among adults. CONCLUSIONS/SIGNIFICANCE:The spatial and temporal patterns identified in this analysis are related to complex environmental, social, and geographic factors. For example, JEV infected patients came from locations with environmental conditions (surface water) that are suitable to support larger mosquito vector populations. Most patients in these data came from villages that are near major roads; likely the result of geographic and financial access to healthcare and also indicating that CNS diseases are underestimated in the region (especially from more remote areas). As Lao PDR is undergoing major developmental and environmental changes, the space-time distributions of the causative agents of CNS infection will also likely change. There is a major need for increased diagnostic abilities; increased access to healthcare, especially for rural populations; and for increased surveillance throughout the nation.

Mosquito-borne flaviviruses with an enzootic transmission cycle like Japanese encephalitis virus (JEV) and West Nile virus (WNV) are a major public health concern. The circulation of JEV in Southeast Asia is well-documented, and the important role of pigs as amplification hosts for the virus is long known. The influence of other domestic animals especially poultry that lives in high abundance and close proximity to humans is not intensively analyzed. Another understudied field in Asia is the presence of the closely related WNV. Such analyses are difficult to perform due to the intense antigenic cross-reactivity between these viruses and the lack of suitable standardized serological assays. The main objective of this study was to assess the prevalence of JEV and WNV flaviviruses in domestic birds, detailed in chickens and ducks, in three different Cambodian provinces. We determined the flavivirus seroprevalence using an hemagglutination inhibition assay (HIA). Additionally, we investigated in positive samples the presence of JEV and WNV neutralizing antibodies (nAb) using foci reduction neutralization test (FRNT). We found 29% (180/620) of the investigated birds positive for flavivirus antibodies with an age-depended increase of the seroprevalence (OR = 1.04) and a higher prevalence in ducks compared to chicken (OR = 3.01). Within the flavivirus-positive birds, we found 43% (28/65) with nAb against JEV. We also observed the expected cross-reactivity between JEV and WNV, by identifying 18.5% double-positive birds that had higher titers of nAb than single-positive birds. Additionally, seven domestic birds (10.7%) showed only nAb against WNV and no nAb against JEV. Our study provides evidence for an intense JEV circulation in domestic birds in Cambodia, and the first serological evidence for WNV presence in Southeast Asia since decades. These findings mark the need for a re-definition of areas at risk for JEV and WNV transmission, and the need for further and intensified surveillance of mosquito-transmitted diseases in domestic animals.

Abstract Background Leptospirosis is an important zoonotic disease worldwide, caused by spirochetes bacteria of the genus Leptospira. In Thailand, cattle and buffalo used in agriculture are in close contact with human beings. During flooding, bacteria can quickly spread throughout an environment, increasing the risk of leptospirosis infection. The aim of this study was to investigate the association of several environmental factors with cattle and buffalo leptospirosis cases in Thailand, with a focus on flooding. Method A total of 3571 urine samples were collected from cattle and buffalo in 107 districts by field veterinarians from January 2011 to February 2013. All samples were examined for the presence of leptospirosis infection by loop-mediated isothermal amplification (LAMP). Environmental data, including rainfall, percentage of flooded area (estimated by remote sensing), average elevation, and human and livestock population density were used to build a generalized linear mixed model. Results A total of 311 out of 3571 (8.43%) urine samples tested positive by the LAMP technique. Positive samples were recorded in 51 out of 107 districts (47.66%). Results showed a significant association between the percentage of the area flooded at district level and leptospirosis infection in cattle and buffalo (p = 0.023). Using this data, a map with a predicted risk of leptospirosis can be developed to help forecast leptospirosis cases in the field. Conclusions Our model allows the identification of areas and periods when the risk of leptospirosis infection is higher in cattle and buffalo, mainly due to a seasonal flooding. The increased risk of leptospirosis infection can also be higher in humans too. These areas and periods should be targeted for leptospirosis surveillance and control in both humans and animals.

ABSTRACT Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily identified in various tick genera originating in China, Jingmenvirus geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification of Jingmen-related viruses in various mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge of the host range, genetic diversity, and geographical distribution of Jingmenviruses by reporting for the first time the identification of Jingmenviruses associated with Rhipicephalus microplus ticks originating in the French Antilles (Guadeloupe and Martinique islands), with Amblyomma testudinarium ticks in Lao PDR, and with Ixodes ricinus ticks in metropolitan France, and from urine of Pteropus lylei bats in Cambodia. Analyses of the relationships between the different Jingmenvirus genomes resulted in the identification of three main phylogenic subclades, each of them containing both tick-borne and mammal-borne strains, reinforcing the idea that Jingmenviruses may be considered as tick-borne arboviruses. Finally, we estimated the prevalence of Jingmenvirus-like infection using luciferase immunoprecipitation assay screening (LIPS) of asymptomatic humans and cattle highly exposed to tick bites. Among 70 French human, 153 Laotian human, and 200 Caribbean cattle sera tested, only one French human serum was found (slightly) positive, suggesting that the prevalence of Jingmenvirus human and cattle infections in these areas is probably low. IMPORTANCE Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae-related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure.

Leptospirosis has been recognized as a major public health concern in Thailand following dramatic outbreaks. We analyzed human leptospirosis incidence between 2004 and 2014 in Mahasarakham province, Northeastern Thailand, in order to identify the agronomical and environmental factors likely to explain incidence at the level of 133 sub-districts and 1982 villages of the province. We performed general additive modeling (GAM) in order to take the spatial-temporal epidemiological dynamics into account. The results of GAM analyses showed that the average slope, population size, pig density, cow density and flood cover were significantly associated with leptospirosis occurrence in a district. Our results stress the importance of livestock favoring leptospirosis transmission to humans and suggest that prevention and control of leptospirosis need strong intersectoral collaboration between the public health, the livestock department and local communities. More specifically, such collaboration should integrate leptospirosis surveillance in both public and animal health for a better control of diseases in livestock while promoting public health prevention as encouraged by the One Health approach.

Objectives: This study aimed to investigate proteinuria occurring during dengue disease in children and assess if measurement of this parameter can help physicians in the clinical management of patients. Methods: Proteinuria was assessed by dipstick and quantified by urine protein:creatinine ratio (UPCR) in samples from patients hospitalized with a confirmed dengue infection and in healthy controls. Results: The dipstick tested positive in 42.9% of the patients presenting at hospital with dengue versus 20.0% in healthy controls. UPCR increased during the critical phase of the disease; peaking one week after fever onset then decreasing as the patients recovered. Patients with warnings signs or severe dengue were more likely to present with proteinuria detected by UPCR at the time of hospital admission compared to patients without warning signs. The sensitivity of this marker, however, was limited as only 16.1% of the patients with warning signs had proteinuria. Conclusions: Urine dipstick and UPCR do not seem to be very valuable for the triage of the patients at the time of the initial consultation but the observation of a decrease of the UPCR during the course of the illness appears to indicate an evolution towards recovery.

Japanese encephalitis virus (JEV) genotype dominance has shifted to genotype I (GI) from genotype III (GIII) in China as demonstrated by molecular epidemiological surveillance. In this study, we performed a serological survey in JEV-non-vaccinated pigs to confirm JEV genotype shift at the sero-epidemiological level. The average ratio of GI/GIII infection was 1.87, suggesting co-circulation of GI and GIII infections with GI infection being more prevalent in pigs in China. To gain an insight into the reasons for this JEV genotype shift, the replication kinetics of seven recently-isolated JEV isolates including three GI strains and four GIII strains were compared in mosquito C6/36 cells, chicken fibroblast cells (DF-1) and porcine iliac artery endothelial cells (PIEC). We observed that GI strains replicated more efficiently than GIII strains in DF-1 and PIEC cells, particularly in DF-1 cells with titers reaching 22.9-225.3 fold higher than GIII strains. This shows an enhanced replication efficiency of GI viruses in avian cells. To examine this enhanced replication efficiency in vivo, young domestic ducklings were used as the animal model and inoculated with GI and GIII strains at day 2 post-hatching. We observed that GI-inoculated ducklings developed higher viremia titers and displayed a comparatively longer viremic duration than GIII-inoculated ducklings. These results conform to the hypothesis of an enhanced replication efficiency for GI viruses in birds. There are 36 amino acid differences between GI and GIII viruses, some of which may be responsible for the enhanced replication efficiency of GI viruses in birds. Based on these findings, we speculated that the enhanced replication of GI viruses in birds would have resulted in higher exposure and therefore infection in mosquitoes, which could result in an increased transmission efficiency of GI viruses in the birds-mosquitoes-birds enzootic transmission cycle, thereby contributing to JEV genotype shift.

As Southeast Asia (SEA) is characterized by high human and domestic animal densities, growing intensification of trade, drastic land use changes and biodiversity erosion, this region appears to be a hotspot to study complex dynamics of zoonoses emergence and health issues at the Animal–Human–Environment interface. Zoonotic diseases and environmental health issues can have devastating socioeconomic and wellbeing impacts. Assessing and managing the related risks implies to take into account ecological and social dynamics at play, in link with epidemiological patterns. The implementation of a One Health (OH) approach in this context calls for improved integration among disciplines and improved cross-sectoral collaboration, involving stakeholders at different levels. For sure, such integration is not achieved spontaneously, implies methodological guidelines and has transaction costs. We explore pathways for implementing such collaboration in SEA context, highlighting the main challenges to be faced by researchers and other target groups involved in OH actions. On this basis, we propose a conceptual framework of OH integration. Throughout 3 components (field-based data management, professional training workshops and higher education), we suggest to develop a new culture of networking involving actors from various disciplines, sectors and levels (from the municipality to the Ministries) through a participatory modelling process, fostering synergies and cooperation. This framework could stimulate long-term dialogue process, based on the combination of case studies implementation and capacity building. It aims for implementing both institutional OH dynamics (multi-stakeholders and cross-sectoral) and research approaches promoting systems thinking and involving social sciences to follow-up and strengthen collective action.

Deforestation and associated changing landscapes are major components of environmental changes, with important implications for ecosystem functioning and biodiversity conservation. Tropical forests are hot spots of biodiversity and provide multiple goods and ecosystem services which benefit people in many ways. Forests also play an important role in health-related legends, myths, and fairy tales from all over the world, and are important sources of new potential emerging microbial threats to humans. Although plausibly numerous abundant microbial forms with a forest origin may exist, our systematic literature review shows that forest-derived infection studies are relatively unexplored, and both taxonomically and geographically biased. Since biodiversity has been associated with emergence of novel infectious diseases at macro-scale, we describe the main biogeographical patterns in the emerging infection-biodiversity-forest loss nexus. Then, we illustrate four fine-scale case studies to decipher the underlying processes of increased infection risk in changing forest clearing landscapes. Finally, we identify scientific challenges and regional management measures required to mitigate these important new emerging threats.

Les forêts intertropicales constituent une source exceptionnelle de diversité biologique spécifique en macro-organismes, mais elles se révèlent être aussi de véritables pépinières en micro-organismes. Ces cinquante dernières années, certains de ces micro-organismes, à l’origine présents chez des animaux forestiers ou hébergés dans l’environnement comme le sol ou l’eau, se sont dévoilés être des agents pathogènes plus ou moins sévères pour les populations humaines exposées. Dans cet article, nous discutons des interactions hôtes-micro-organismes rencontrées dans les forêts primaires en les abordant tant d’un angle macroécologique que d’un point de vue plus fonctionnel, en l’illustrant de quatre exemples d’agents microbiens émergents. Plus que tout autre déterminant, les modifications d’usages des sols, notamment au travers de la déforestation pour le développement d’une agriculture, et les contacts avec les micro-organismes via la biodiversité, particulièrement lors de la pratique de chasse, exposent des individus susceptibles à ces nouveaux dangers micro-biens. Avec la déforestation et des expositions croissantes avec la faune sauvage, le risque de nouvelles infections humaines devient une réalité internationale exigeant de la part des autorités publiques de mieux prendre en considération ces éléments pour la sécurité sanitaire mondiale.

Japanese encephalitis is mainly considered a rural disease, but there is growing evidence of a peri-urban and urban transmission in several countries, including Cambodia. We, therefore, compared the epidemiologic dynamic of Japanese encephalitis between a rural and a peri-urban setting in Cambodia. We monitored two cohorts of 15 pigs and determined the force of infection-rate at which seronegative pigs become positive-in two study farms located in a peri-urban and rural area, respectively. We also studied the mosquito abundance and diversity in proximity of the pigs, as well as the host densities in both areas. All the pigs seroconverted before the age of 6 months. The force of infection was 0.061 per day (95% confidence interval = 0.034-0.098) in the peri-urban cohort and 0.069 per day (95% confidence interval = 0.047-0.099) in the rural cohort. Several differences in the epidemiologic dynamic of Japanese encephalitis between both study sites were highlighted. The later virus amplification in the rural cohort may be linked to the later waning of maternal antibodies, but also to the higher pig density in direct proximity of the studied pigs, which could have led to a dilution of mosquito bites at the farm level. The force of infection was almost identical in both the peri-urban and the rural farms studied, which shifts the classic epidemiologic cycle of the virus. This study is a first step in improving our understanding of Japanese encephalitis virus ecology in different environments with distinct landscapes, human and animal densities.

Japanese Encephalitis (JE) is the most important cause of human encephalitis throughout Asia and the Pacific. Although JE is a vector-borne disease, it has been demonstrated experimentally that transmission between pigs can occur through direct contact. Whether pig-to-pig transmission plays a role in the natural epidemiological cycle of JE remains unknown. To assess whether direct transmission between pigs may occur under field conditions, we built two mathematical models of JE transmission incorporating vector-borne transmission alone or a combination of vector-borne and direct transmission. We used Markov Chain Monte Carlo (MCMC) techniques to estimate the parameters of the models. We fitted the models to (i) two serological datasets collected longitudinally from two pig cohorts (C1 and C2) during two periods of four months on a farm on the outskirts of Phnom-Penh, Cambodia and to (ii) a cross-sectional (CS) serological survey dataset collected from 505 swine coming from eight different provinces of Cambodia. In both cases, the model incorporating both vector-borne and direct transmission better explained the data. We computed the value of the basic reproduction number R0 (2.93 for C1, 2.66 for C2 and 2.27 for CS), as well as the vector-borne reproduction number Rpv and the direct transmission reproduction number Rpp. We then determined the contribution of direct transmission on R0 (11.90% for C1, 11.62% for C2 and 7.51% for CS). According to our results, the existence of pig-to-pig transmission is consistent with our swine serological data. Thus, direct transmission may contribute to the epidemiological cycle of JE in Cambodia. These results need to be confirmed in other eco-climatic settings, in particular in temperate areas where pig-to-pig transmission may facilitate the persistence of JE virus (JEV) during cold seasons when there are no or few mosquitoes.

Cave roosting bats represent an important component of Southeast Asian bat diversity and are vulnerable to human disturbance during critical reproductive periods (pregnancy, lactation and weaning). Because dramatic growth of cave tourism in recent decades has raised concerns about impacts on cave bats in the region, we assessed the reproductive phenology of two insectivorous species (Hipposideros larvatus sensu lato and Taphozous melanopogon) at three caves in Cambodia for 23 months in 2014-2016 and evaluated human visitation to these sites between 2007 and 2014. Despite the differing foraging strategies employed by the two taxa, the temporal consistency observed in proportions of pregnant, lactating and juvenile bats indicates that their major birth peaks coincide with the time of greatest cave visitation annually, particularly for domestic visitors and namely during the Cambodian new year in April. They also reflect rainfall patterns and correspond with the reproductive phenology of insectivorous cave bats in Vietnam. These findings were predictable because 1) insect biomass and thus food availability for insectivorous bats are optimal for ensuring survival of young following this period, and 2) the Khmer new year is the most significant month for religious ceremonies and thus domestic cave visitation nationally, due to the abundance of Buddhist shrines and temples in Cambodian caves. While the impact of visitor disturbance on bat population recruitment cannot be empirically assessed due to lack of historical data, it is nonetheless likely to have been considerable and raises a conservation concern. Further, because growing evidence suggests that insectivorous cave bats exhibit reproductive synchrony across continental Southeast Asia where countless cave shrines are heavily frequented during April in Theravada Buddhist countries (e.g., Myanmar, Thailand, Cambodia and Laos), our results may have wider applicability in the region. We consequently advocate for increased emphasis on sustainable cave management practices in Cambodia and further investigations to determine whether our findings present a broader concern for cave bat conservation in Southeast Asia.

Remote sensing can contribute to early warning for diseases with environmental drivers, such as flooding for leptospirosis. In this study we assessed whether and which remotely-sensed flooding indicator could be used in Cambodia to study any disease for which flooding has already been identified as an important driver, using leptospirosis as a case study. The performance of six potential flooding indicators was assessed by ground truthing. The Modified Normalized Difference Water Index (MNDWI) was used to estimate the Risk Ratio (RR) of being infected by leptospirosis when exposed to floods it detected, in particular during the rainy season. Chi-square tests were also calculated. Another variable-the time elapsed since the first flooding of the year-was created using MNDWI values and was also included as explanatory variable in a generalized linear model (GLM) and in a boosted regression tree model (BRT) of leptospirosis infections, along with other explanatory variables. Interestingly, MNDWI thresholds for both detecting water and predicting the risk of leptospirosis seroconversion were independently evaluated at -0.3. Value of MNDWI greater than -0.3 was significantly related to leptospirosis infection (RR = 1.61 [1.10-1.52]; χ2 = 5.64, p-value = 0.02, especially during the rainy season (RR = 2.03 [1.25-3.28]; χ2 = 8.15, p-value = 0.004). Time since the first flooding of the year was a significant risk factor in our GLM model (p-value = 0.042). These results suggest that MNDWI may be useful as a risk indicator in an early warning remote sensing tool for flood-driven diseases like leptospirosis in South East Asia.

Despite the increased use of vaccination in several Asian countries, Japanese Encephalitis (JE) remains the most important cause of viral encephalitis in Asia in humans with an estimated 68,000 cases annually. Considered a rural disease occurring mainly in paddy-field dominated landscapes where pigs are amplifying hosts, JE may nevertheless circulate in a wider range of environment given the diversity of its potential hosts and vectors. The main objective of this study was to assess the intensity of JE transmission to pigs in a peri-urban environment in the outskirt of Phnom Penh, Cambodia. We estimated the force of JE infection in two cohorts of 15 sentinel pigs by fitting a generalised linear model on seroprevalence monitoring data observed during two four-month periods in 2014. Our results provide evidence for intensive circulation of JE virus in a periurban area near Phnom Penh, the capital and most populated city of Cambodia. Understanding JE virus transmission in different environments is important for planning JE virus control in the long term and is also an interesting model to study the complexity of vector-borne diseases. Collecting quantitative data such as the force of infection will help calibrate epidemiological model that can be used to better understand complex vector-borne disease epidemiological cycles.

The 1957 and 1968 influenza pandemics, each of which killed ≈1 million persons, arose through reassortment events. Influenza virus in humans and domestic animals could reassort and cause another pandemic. To identify geographic areas where agricultural production systems are conducive to reassortment, we fitted multivariate regression models to surveillance data on influenza A virus subtype H5N1 among poultry in China and Egypt and subtype H3N2 among humans. We then applied the models across Asia and Egypt to predict where subtype H3N2 from humans and subtype H5N1 from birds overlap; this overlap serves as a proxy for co-infection and in vivo reassortment. For Asia, we refined the prioritization by identifying areas that also have high swine density. Potential geographic foci of reassortment include the northern plains of India, coastal and central provinces of China, the western Korean Peninsula and southwestern Japan in Asia, and the Nile Delta in Egypt.

The maintenance mechanisms of ebolaviruses in African forest ecosystems are still unknown, but indirect evidences point at the involvement of some bat species. Despite intense research, the main bat-maintenance hypothesis has not been confirmed yet. The alternative hypotheses of a non-bat maintenance host or a maintenance community including, or not, several bat and other species, deserves more investigation. However, African forest ecosystems host a large biodiversity and abound in potential maintenance hosts. How does one puzzle out? Since recent studies have revealed that several bat species have been exposed to ebolaviruses, the common denominator to these hypotheses is that within the epidemiological cycle, some bats species must be exposed to the viruses and infected by these potential alternative hosts. Under this constraint, and given the peculiar ecology of bats (roosting behaviour, habitat utilisation, and flight mode), we review the hosts and transmission pathways that can lead to bat exposure and infection to ebolaviruses. In contrast to the capacity of bats to transmit ebolaviruses and other pathogens to many hosts, our results indicate that only a limited number of hosts and pathways can lead to the transmission of ebolaviruses to bats, and that the alternative maintenance host, if it exists, must be amongst them. A list of these pathways is provided, along with protocols to prioritise and investigate these alternative hypotheses. In conclusion, taking into account the ecology of bats and their known involvement in ebolaviruses ecology drastically reduces the list of potential alternative maintenance hosts for ebolaviruses. Understanding the natural history of ebolaviruses is a health priority, and investigating these alternative hypotheses could complete the current effort focused on the role of bats.

Wildlife populations in Southeast Asia are subject to increasing pressure from climate change, habitat loss and human disturbance. Cave-roosting bats are particularly vulnerable to all three factors. Because of the ecological services they provide, it is important to assess specific vulnerabilities to inform their conservation management. We evaluated the reproductive phenology and body condition of Chaerephon plicatus for 14 months in 2015–2016 and quantified guano harvesting at the largest colony in Cambodia in 2011–2016. As in Thailand and Myanmar, two annual breeding cycles were recorded, characterized as continuous bimodal polyoestry, with parturition primarily occurring in April and October. Significant declines occurred in body condition between the late wet season and the late dry season, suggesting that bats experience increasing energetic stress as the dry season progresses. Annual guano harvests increased over the study period but could not be used as a proxy for monitoring population size due to the loss of unknown amounts during the wet season and unquantified movements of bats between C. plicatus colonies in the region. We recommend studies to determine the scale and drivers of such movements and creation of sustainable guano harvesting and population monitoring initiatives to ensure the conservation of C. plicatus colonies in Cambodia.

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.

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.

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.

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.

The potential existence of a wild bird reservoir for highly pathogenic avian influenza (HPAI) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses, responsible for concurrent outbreaks in migratory and domestic birds over Asia, Europe, and Africa. During a large-scale surveillance programme over Eastern Europe, the Middle East, and Africa, we detected avian influenza viruses of H5N2 subtype with a highly pathogenic (HP) viral genotype in healthy birds of two wild waterfowl species sampled in Nigeria. We monitored the survival and regional movements of one of the infected birds through satellite telemetry, providing a rare evidence of a non-lethal natural infection by an HP viral genotype in wild birds. Phylogenetic analysis of the H5N2 viruses revealed close genetic relationships with H5 viruses of low pathogenicity circulating in Eurasian wild and domestic ducks. In addition, genetic analysis did not reveal known gallinaceous poultry adaptive mutations, suggesting that the emergence of HP strains could have taken place in either wild or domestic ducks or in non-gallinaceous species. The presence of coexisting but genetically distinguishable avian influenza viruses with an HP viral genotype in two cohabiting species of wild waterfowl, with evidence of non-lethal infection at least in one species and without evidence of prior extensive circulation of the virus in domestic poultry, suggest that some strains with a potential high pathogenicity for poultry could be maintained in a community of wild waterfowl.