The genetic diversity of Nipah virus across spatial scales.

BACKGROUND: Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity. METHODS: We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). We divide the four major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area. RESULTS: We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500-2000km2. We estimate that each genetic cluster occupies an average area of 1.3million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only ∼15% of overall NiV diversity has been uncovered. CONCLUSION: Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales.

Evisceration with implantation of an intrascleral silicone prosthesis in dogs: A retrospective study of 107 cases (2010-2019).

OBJECTIVE: To retrospectively analyze the preoperative clinical characteristics and surgical outcomes of evisceration with implantation of an intrascleral silicone prosthesis (EIISP) procedures in dogs and evaluate whether brachycephalic dogs are more prone than non-brachycephalic dogs to develop postoperative complications after EIISP. ANIMAL STUDIED: Ninety-One dogs (19 of which were brachycephalic) were included. PROCEDURES: Medical records from 2010 to 2019 were reviewed. Signalment, reason for EIISP, postoperative complications, follow-up time, and postoperative eye appearance were analyzed. RESULTS: The most frequently represented breeds were French Bulldog [11/91 (12%) dogs], Jack Russell Terrier [6/91 (7%)], and Shih Tzu [6/91 (7%)]. Brachycephalic dogs were statistically younger than non-brachycephalic dogs at the time of EIISP (p = 1.61 × 10-5 ). Uncontrolled glaucoma was the most common reason for EIISP in both groups. Short-term complications (from D0 to D15) seen in 7/91 (8%) dogs included epithelial corneal ulcers (n = 3), keratoconjunctivitis sicca (KCS) (n = 2), and prosthesis extrusion (n = 2). Long-term complications seen in 26/91 (29%) dogs included KCS (n = 11), epithelial corneal ulcers (n = 7), stromal ulcers (n = 3), entropion (n = 4), and prosthesis extrusion (n = 1). Extrusion of the prosthesis occurred twice in eyes that had undergone diode laser transscleral cyclophotocoagulation. The risk of postoperative complications was not significantly different between brachycephalic and non-brachycephalic dogs (p = .3). CONCLUSIONS: Brachycephalic status in dogs does not appear to influence the risk of complications from EIISP. Nevertheless, the present study is a reminder that EIISP focuses on esthetics, and considering the possible complications associated with it, it does not provide a benefit to the patient compared to enucleation.

Effect of an ear cleaner instillation containing lipacids in a model of re-acidification of the external auditory canal in dogs.

BACKGROUND: In humans, the acidic pH of the ear canal plays a protective role against infection and a change towards alkalinity of the external auditory canal (EAC) is a local factor in the progression of acute to chronic otitis externa (OE). The use of acidic preparations alone for treatment of OE without concurrent antibiotic use is well-documented in humans. In dogs, only one study has investigated the EAC pH in healthy dogs and in dogs with OE, and investigations to understand the role of EAC pH in the pathogenesis of canine OE are lacking. HYPOTHESIS/OBJECTIVES: To obtain physiological EAC pH values in beagle dogs. To develop a model of re-acidification of the EAC in dogs and to investigate how an acidic solution may accelerate the return to a physiological pH. ANIMALS: Ten healthy beagle dogs in a laboratory setting. MATERIALS AND METHODS: A model of re-acidification of the EAC was developed by instillation of a pH 10.1 phosphate-buffered saline (PBS) solution and the subsequent acidic effect of an ear cleaner containing lipacids was evaluated in this model. RESULTS: Mean physiological EAC pH was 6.12 (± 0.36). EAC re-acidification took up to 9 h in this model. Mean pH values dropped immediately to 6.38 (± 0.27) on ears treated with an acidic ear cleaner. No abrupt drop was observed of the mean pH values for the control ears. CONCLUSION AND CLINICAL IMPORTANCE: This study confirms that physiological EAC pH in dogs is acidic. This model of re-acidification of the EAC pH allows investigations on acidic properties of topical ear products in healthy ears.

Contexte - Chez l'homme, le pH acide du conduit auditif joue un rôle protecteur contre l'infection et l'évolution vers l'alcalinité du conduit auditif externe (CAE) et est un facteur local de progression de l'otite externe (OE) aiguë à chronique. L'utilisation de préparations acides seules pour le traitement de l'OE sans utilisation concomitante d'antibiotiques est bien documentée chez l'homme. Chez les chiens, une seule étude a étudié le pH du CAE chez les chiens en bonne santé et chez les chiens atteints d'OE, et les recherches pour comprendre le rôle du pH du CAE dans la pathogenèse de l'OE canine font défaut. Hypothèses/objectifs - Obtenir des valeurs physiologiques de pH du CAE chez des chiens beagle. Développer un modèle de réacidification du CAE chez le chien et étudier comment une solution acide peut accélérer le retour à un pH physiologique. Animaux - Dix chiens beagle de laboratoire en bonne santé. Matériels et méthodes - Un modèle de réacidification du CAE a été développé par instillation d'une solution saline tamponnée (PBS) à pH 10,1 et l'effet acide ultérieur d'un nettoyant pour oreilles contenant des lipacides a été évalué dans ce modèle. Résultats - Le pH physiologique moyen du CAE était de 6,12 (± 0,36). La réacidification du CAE a pris jusqu'à 9 h dans ce modèle. Les valeurs moyennes du pH chutent immédiatement à 6,38 (± 0,27) sur les oreilles traitées avec un nettoyant auriculaire acide. Aucune chute brutale n'a été observée des valeurs moyennes de pH pour les oreilles témoins. Conclusion et importance clinique - Cette étude confirme que le pH physiologique du CAE chez le chien est acide. Ce modèle de réacidification du pH du CAE permet des investigations sur les propriétés acides des produits topiques auriculaires dans des oreilles saines.

Introducción; en humanos, el pH ácido del canal auditivo juega un papel protector contra la infección y un cambio hacia la alcalinidad del canal auditivo externo (EAC) es un factor local en la progresión de la otitis externa (OE) aguda a crónica. El uso de preparaciones ácidas solas para el tratamiento de la OE sin el uso concomitante de antibióticos está bien documentado en humanos. En perros, solo un estudio ha investigado el pH de EAC en perros sanos y en perros con OE, y faltan investigaciones para comprender el papel del pH de EAC en la patogenia de la OE canina. Hipótesis/objetivos - Obtener valores de pH fisiológico de EAC en perros beagle. Desarrollar un modelo de reacidificación del EAC en perros e investigar cómo una solución ácida puede acelerar el retorno a un pH fisiológico. Animales- diez perros beagle sanos en un laboratorio. Materiales y métodos- se desarrolló un modelo de reacidificación del EAC mediante la instilación de una solución salina tamponada con fosfato (PBS) de pH 10,1 y se evaluó en este modelo el efecto ácido subsiguiente de un limpiador de oídos que contenía lípidos. Resultados - El pH fisiológico medio del EAC fue de 6,12 (± 0,36). La reacidificación de EAC tomó hasta 9 h en este modelo. Los valores medios de pH cayeron inmediatamente a 6,38 (± 0,27) en los oídos tratados con un limpiador de oídos ácido. No se observó una caída abrupta de los valores medios de pH para los oíds de control. Conclusión e importancia clínica- este estudio confirma que el pH fisiológico de EAC en perros es ácido. Este modelo de reacidificación del pH de EAC permite realizar investigaciones sobre las propiedades ácidas de los productos tópicos para el oído en oídos sanos.

Contexto - Em humanos, o pH ácido do conduto auditivo exerce uma grande função protetora contra infecções e a alcalinização do conduto auditivo externo (CAE) é um fator local de progressão de otite externa (OE) aguda para crônica. A utilização unicamente de formulações ácidas para o tratamento de OE sem a utilização concomitante de antibióticos é bem documentada em humanos. Em cães, apenas um estudo investigou o pH do CAE em cães saudáveis com OE, e são escassas as pesquisas investigando o papel do pH do CAE na patogênese da OE. Hipótese/objetivos - Se obter os valores fisiológicos do pH dos CAEs de cães Beagle. Desenvolver um modelo de re-acidificação do CAE em cães e investigar como uma solução ácida pode acelerar o retorno ao pH fisiológico original. Animais - Dez cães Beagle saudáveis de laboratório. Materiais e Métodos - Um modelo de re-acidificação do CAE foi desenvolvido por instilação de solução salina tamponada com fosfato (PBS) com um pH 10,1 e o efeito acidificante subsequente de um limpador de ouvido contendo ácidos lipídicos foi avaliado neste modelo. Resultados - O pH fisiológico médio do CAE foi de 6,12 (± 0,36). A re-acidificação do CAE levou até 9h neste modelo. Os valores médios de pH caíram imediatamente para 6,38 (± 0,27) nas orelhas tratadas com um limpador otológico ácido. Não foi observada queda abrupta dos valores médios de pH para as orelhas controle. Conclusão e importância clínica - Este estudo confirmou que o pH fisiológico do CAE de cães é ácido. Este modelo de re-acidificação do pH do CAE permite investigações sobre as propriedades acidificantes de produtos otológicos tópicos para orelhas saudáveis.

Nipah virus circulation at human-bat interfaces, Cambodia.

OBJECTIVE: To better understand the potential risks of Nipah virus emergence in Cambodia by studying different components of the interface between humans and bats. METHODS: From 2012 to 2016, we conducted a study at two sites in Kandal and Battambang provinces where fruit bats (Pteropus lylei) roost. We combined research on: bat ecology (reproductive phenology, population dynamics and diet); human practices and perceptions (ethnographic research and a knowledge, attitude and practice study); and Nipah virus circulation in bat and human populations (virus monitoring in bat urine and anti-Nipah-virus antibody detection in human serum). FINDINGS: Our results confirmed circulation of Nipah virus in fruit bats (28 of 3930 urine samples positive by polymerase chain reaction testing). We identified clear potential routes for virus transmission to humans through local practices, including fruit consumed by bats and harvested by humans when Nipah virus is circulating, and palm juice production. Nevertheless, in the serological survey of 418 potentially exposed people, none of them were seropositive to Nipah virus. Differences in agricultural practices among the regions where Nipah virus has emerged may explain the situation in Cambodia and point to actions to limit the risks of virus transmission to humans. CONCLUSION: Human practices are key to understanding transmission risks associated with emerging infectious diseases. Social science disciplines such as anthropology need to be integrated in health programmes targeting emerging infectious diseases. As bats are hosts of major zoonotic pathogens, such integrated studies would likely also help to reduce the risk of emergence of other bat-borne diseases.

A moisturizer formulated with glycerol and propylene glycol accelerates the recovery of skin barrier function after experimental disruption in dogs.

BACKGROUND: Moisturizers are foundational therapies for human atopic dermatitis. In veterinary medicine, the use of moisturizers has been recommended by an expert committee to alleviate skin dryness that would occur, for example, in canine atopic dermatitis (cAD). However, little is known regarding the effects of moisturizers on the skin barrier. HYPOTHESIS/OBJECTIVES: To investigate the effects of a moisturizer on skin barrier recovery in a canine model of chronic mechanical barrier disruption. ANIMALS: Six healthy beagle dogs maintained in a laboratory setting. METHODS AND MATERIALS: A model of chronic skin barrier disruption was simulated by tape stripping on both sides of the thorax. The moisturizer then was applied twice daily for one week to one side of the thorax, while the other hemithorax was left untreated. The effects were evaluated by measurement of transepidermal water loss (TEWL) at various times during skin barrier recovery, and by histological assessment of the disrupted skin one week after moisturizer application. RESULTS: Overall, TEWL was reduced, epidermal thickness was lower, stratum corneum thickness was greater and the intensity of the dermal inflammatory infiltrate was reduced for treated sites. CONCLUSIONS AND CLINICAL IMPORTANCE: These results suggest a potential benefit of the moisturizer for improving skin barrier function, which is frequently altered in chronic inflammatory dermatoses such as cAD.

Extreme temperature event and mass mortality of insectivorous bats.

A mass mortality event involving Chaerephon plicatus and Taphozous theobaldi bats occurred during a heat wave in April 2016 in Cambodia. This was investigated to clarify the causes of the die-off and assess the risk to public health. Field evidences, clinical signs, and gross pathology findings were consistent with a heat stress hypothesis. However, the detection of a novel bat paramyxovirus raises questions about its role as a contributing factor or a coincidental finding. Systematic documentation of bat die-offs related to extreme weather events is necessary to improve understanding of the effect of changing weather patterns on bat populations and the ecosystem services they provide.

[Tropical forests, changes in land uses and emerging infectious hazards]. / Forêts tropicales, changements d'usage des sols et risques infectieux émergents.

Tropical forests have the greatest biodiversity in macroorganisms on the planet, and they are also the richest in myriads of microorganisms for which so little is known today. Over the last 50 years, many of these microbial forms, that are naturally embedded into wildlife or the environment, e.g. soil, water, have revealed to be more or less dangerous pathogens for people exposed to these new natural threats, i.e. emerging infectious diseases. Here, we discuss about the extraordinary diversity of microorganisms that are present in tropical rainforests. We first present the main global distribution patterns for microbial forms at the interface between tropical wildlife and human, and second we provide an epidemiological picture on how microbial transmission from wild animals or the environment to people operates in tropical areas through four case-studies. We examine the animal hosts or environment, and transmission mechanisms involved in spillover of zoonotic or environmentally-persistent microbes, and identify land-use changes through deforestation for the development of agriculture, and contacts with wildlife notably through bush meat hunting as major drivers that facilitate mixing of diverse animal hosts and their microbial communities with human during practices. With an increase of deforestation in the tropics and more contacts between wildlife and people, new emerging disease events with high epidemic and pandemic potential will happen, that should guide new health policies and strategies at the global scale.

Rabies Postexposure Prophylaxis Noncompletion After Dog Bites: Estimating the Unseen to Meet the Needs of the Underserved.

Postexposure prophylaxis (PEP) prevents human rabies and is accessible in Cambodia principally in Phnom Penh, the capital. Timely, affordable access to PEP is a challenge for the mainly rural population. We aimed to identify districts independently associated with PEP noncompletion to position frontline vaccination centers. We analyzed the 2009-2013 database at the Rabies Prevention Center at the Institut Pasteur du Cambodge, Phnom Penh. Logistic regressions identified nongeographic determinants of PEP noncompletion as well as the districts that were independently associated with noncompletion after adjustment for these determinants. The influence of distance by road was estimated using a boosted regression-trees model. We computed a population attributable fraction (rabies index (RI)) for each district and developed a map of this RI distribution. A cartographic analysis based on the statistic developed by Getis and Ord identified clusters of high-RI districts. Factors independently associated with noncompletion were patients' district of residence, male sex, age 15-49 years, initial visit during rice harvest, the dog's status (culled or disappeared), and a prescribed PEP protocol requiring more than 3 PEP sessions (4 or 5). Four clusters of high-RI districts were identified using this analytical strategy, which is applicable to many vaccination or other health services. Positioning frontline PEP centers in these districts could significantly widen access to timely and adequate PEP.

A remotely sensed flooding indicator associated with cattle and buffalo leptospirosis cases in Thailand 2011-2013.

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.

Isolation and full-genome sequences of Japanese encephalitis virus genotype I strains from Cambodian human patients, mosquitoes and pigs.

Japanese encephalitis remains the most important cause of viral encephalitis in humans in several southeast Asian countries, including Cambodia, causing at least 65 000 cases of encephalitis per year. This vector-borne viral zoonosis - caused by Japanese encephalitis virus (JEV) - is considered to be a rural disease and is transmitted by mosquitoes, with birds and pigs being the natural reservoirs, while humans are accidental hosts. In this study we report the first two JEV isolations in Cambodia from human encephalitis cases from two studies on the aetiology of central nervous system disease, conducted at the two major paediatric hospitals in the country. We also report JEV isolation from Culextritaeniorhynchus mosquitoes and from pig samples collected in two farms, located in peri-urban and rural areas. Out of 11 reverse-transcription polymerase chain reaction-positive original samples, we generated full-genome sequences from 5 JEV isolates. Five additional partial sequences of the JEV NS3 gene from viruses detected in five pigs and one complete coding sequence of the envelope gene of a strain identified in a pig were generated. Phylogenetic analyses revealed that JEV detected in Cambodia belonged to genotype I and clustered in two clades: genotype I-a, mainly comprising strains from Thailand, and genotype I-b, comprising strains from Vietnam that dispersed northwards to China. Finally, in this study, we provide proof that the sequenced JEV strains circulate between pigs, Culex tritaeniorhynchus and humans in the Phnom Penh vicinity.

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.

Seroprevalence and renal carriage of pathogenic Leptospira in livestock in Cotonou, Benin.

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.

Predicting hotspots for influenza virus reassortment.

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.

Assessment of inter-observer agreement among experienced and inexperienced observers and an automated device for dipstick urinalysis in dogs and cats.

Standard visual urine dipstick analysis (UDA) is performed routinely in veterinary medicine; results can be influenced by both the operator and the method. We evaluated the agreement of results for canine and feline urine samples analyzed using a 10-patch dipstick (Multistix10SG; Siemens), both visually under double-anonymized conditions by students and a laboratory technician, and with an automated device (AD; Clinitek Status, Siemens). The mean concordance for semiquantitative urinalysis results between students and the technician and between students and the AD was fair (κ0.21-0.40) in dogs and cats; concordance was moderate between the technician and the AD (κ0.41-0.60) in dogs and good (κ0.61-0.80) in cats. For pH, the mean concordance between students and the technician and between the technician and the AD was good (ρ0.80-0.92) in dogs and cats; concordance was good between students and the AD (ρ0.80-0.92) in dogs and moderate (ρ0.59-0.79) in cats. Repeatability was higher (p < 0.001) for the technician and the AD than for a student. We found good agreement between UDA performed by an experienced operator and an AD in dogs and cats but found low reproducibility and low repeatability for urinalysis performed by an inexperienced operator.

Assessment of virus and Leptospira carriage in bats in France.

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 ß-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.

Foraging and mating behaviors of Hypsignathus monstrosus at the bat-human interface in a central African rainforest.

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.

The genetic diversity of Nipah virus across spatial scales.

Nipah virus (NiV), a highly lethal virus in humans, circulates silently in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining genomes from bats means we have a poor understanding of NiV diversity, including how many lineages circulate within a roost and the spread of NiV over increasing spatial scales. Here we develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). In Bangladesh, where most human infections occur, we find evidence of increased spillover risk from one of the two co-circulating sublineages. We divide the four major NiV sublineages into 15 genetic clusters (emerged 20-44 years ago). Within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1,500-2,000 km2. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate that each genetic cluster occupies an average area of 1.3 million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000 km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most of the genetic clusters have been identified, but only ~15% of overall NiV diversity has been uncovered. Our findings are consistent with entrenched co-circulation of distinct lineages, even within individual roosts, coupled with slow migration over larger spatial scales.

Spatial-temporal patterns and risk factors for human leptospirosis in Thailand, 2012-2018.

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.

Circulating serogroups of Leptospira in swine from a 7-year study in France (2011-2017).

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.

Quantification and characterisation of commensal wild birds and their interactions with domestic ducks on a free-range farm in southwest France.

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.