Managing the challenges of a highly pathogenic avian influenza H5N8 outbreak in Uganda: a case study.

In 2016-2017, the H5N8 strain of highly pathogenic avian influenza (HPAI) spread worldwide and Uganda reported the first occurrence of the disease in its poultry and wild birds. Genetic analysis revealed that the virus clusters with 2.3.4.4 group B strains from birds in central and southern Asia, and thus forms part of the 2.3.4.4 group B clade. Since Uganda is in the path of two major migratory bird flyways, it is likely that infected migratory wild birds played a crucial role in the introduction of H5N8 HPAI viruses into Uganda. The outbreaks happened in the districts of Wakiso, Masaka and Kalangala and affected domestic and wild birds. A One Health Multisectoral Coordination Committee, consisting of a National Task Force, Technical Working Groups and District Disaster Management Committees, was immediately activated to coordinate the preparedness and response efforts to control the disease. In all the affected districts, surveillance was intensified on both domestic and wild birds; biosecurity measures were increased; and movement controls, culling, cleaning, disinfection and safe disposal of carcasses were implemented. Awareness of the disease was raised through education materials, leaflets and brochures distributed to farmers. Finally, Uganda successfully controlled the H5N8 outbreak, using its national preparedness and response mechanisms and through collaboration with international partners. The emergence and spread of this virus strain in Uganda and other parts of Africa poses a significant threat to the poultry industry and food security.

En 2016­2017, le sous-type H5N8 du virus de l'influenza aviaire hautement pathogène (IAHP) s'est propagé dans le monde entier. En Ouganda, les premiers cas ont été notifiés chez les volailles et dans l'avifaune. Une analyse génétique a montré que le virus causal était relié aux souches 2.3.4.4 de groupe B trouvées chez des oiseaux d'Asie centrale et du Sud et qu'il appartenait donc au clade 2.3.4.4 des virus du groupe B. L'Ouganda se trouvant sur le tracé de deux voies majeures de migration d'oiseaux, les espèces sauvages d'oiseaux migrateurs ont probablement joué un rôle déterminant dans l'introduction des virus H5N8 de l'IAHP en Ouganda. Les foyers se sont déclarés dans les districts de Wakiso, Masaka et Kalangala, affectant des espèces aviaires domestiques et sauvages. Un Comité de coordination multisectoriel Une seule santé a aussitôt été créé, composé d'un groupe de travail national, de plusieurs groupes techniques d'experts et de comités locaux de gestion des urgences, afin d'assurer la coordination des activités de préparation et de réponse pour lutter contre la maladie. La surveillance des oiseaux domestiques et de l'avifaune a été intensifiée dans tous les districts affectés ; les mesures de biosécurité ont été renforcées ; les mouvements d'animaux ont été soumis à un contrôle ; enfin, des mesures d'abattage, de nettoyage/désinfection et d'élimination sécurisée des cadavres ont été introduites. Une campagne de sensibilisation à la maladie a été organisée avec la distribution aux éleveurs de matériels pédagogiques, dépliants et brochures d'information. L'Ouganda a finalement réussi à contrôler ce foyer dû au virus H5N8 en appliquant les mécanismes nationaux de préparation et de réponse, avec la collaboration de ses partenaires internationaux. L'émergence et la propagation de cette souche virale en Ouganda et dans d'autres régions d'Afrique font peser une lourde menace sur le secteur des productions avicoles ainsi que sur la sécurité alimentaire.

En los años 2016 y 2017 la cepa H5N8 del virus de la influenza aviar altamente patógena (IAAP) se diseminó por el mundo entero y Uganda notificó su primera aparición en las poblaciones de aves salvajes y de corral del país. El análisis genético reveló que el virus se agrupa con cepas 2.3.4.4 del grupo B que se encuentran en aves de Asia central y meridional, de donde se sigue que forma parte del clado 2.3.4.4 del grupo B. Toda vez que por el territorio ugandés pasan dos grandes rutas migratorias, es probable que, en el curso de sus migraciones, ciertas aves salvajes infectadas hayan tenido un papel decisivo en la introducción en el país del virus H5N8 de la IAAP. Los brotes tuvieron lugar en los distritos de Wakiso, Masaka y Kalangala y afectaron a aves tanto domésticas como salvajes. Inmediatamente se activó un comité de coordinación multisectorial de Una sola salud, formado por un grupo de trabajo nacional más una serie de grupos de trabajos técnicos y de comités de distrito de «gestión de catástrofes¼, que tenía por cometido coordinar las actividades de preparación y respuesta para combatir la enfermedad. En todos los distritos afectados se intensificó la vigilancia de las aves domésticas y salvajes, se reforzaron las medidas de seguridad biológica y se instituyeron medidas de control de los movimientos, sacrificio sanitario, limpieza, desinfección y eliminación segura de los animales muertos. También se repartieron entre los productores material pedagógico, prospectos y folletos con el objetivo de dar mejor a conocer la enfermedad. A la postre Uganda, gracias a sus mecanismos nacionales de preparación y respuesta, aunados a la colaboración con contrapartes internacionales, logró controlar el brote causado por el virus H5N8. La aparición y propagación de esta cepa vírica en Uganda y otras partes de África supone una importante amenaza para el sector avícola y la seguridad alimentaria.

Hepatitis E virus infection in North Italy: high seroprevalence in swine herds and increased risk for swine workers.

We determined the hepatitis E virus (HEV) seroprevalence and detection rate in commercial swine herds in Italy's utmost pig-rich area, and assessed HEV seropositivity risk in humans as a function of occupational exposure to pigs, diet, foreign travel, medical history and hunting activities. During 2011-2014, 2700 sera from 300 swine herds were tested for anti-HEV IgG. HEV RNA was searched in 959 faecal pools from HEV-seropositive herds and in liver/bile/muscle samples from 179 pigs from HEV-positive herds. A cohort study of HEV seropositivity in swine workers (n = 149) was also performed using two comparison groups of people unexposed to swine: omnivores (n = 121) and vegetarians/vegans (n = 115). Herd-level seroprevalence was 75·6% and was highest in farrow-to-feeder herds (81·6%). Twenty-six out of 105 (24·8%) herds had HEV-positive faecal samples (25 HEV-3, one HEV-4). Only one bile sample tested positive. HEV seropositivity was 12·3% in swine workers, 0·9% in omnivores and 3·0% in vegetarians/vegans. Factors significantly associated with HEV seropositivity were occupational exposure to pigs, travel to Africa and increased swine workers' age. We concluded that HEV is widespread in Italian swine herds and HEV-4 circulation is alarming given its pathogenicity, with those occupationally exposed to pigs being at increased risk of HEV seropositivity.

Serological evidence of H9N2 avian influenza virus exposure among poultry workers from Fars province of Iran.

BACKGROUND: Since the 1990s, influenza A viruses of the H9N2 subtype have been causing infections in the poultry population around the globe. This influenza subtype is widely circulating in poultry and human cases of AI H9N2 have been sporadically reported in countries where this virus is endemic in domestic birds. The wide circulation of H9N2 viruses throughout Europe and Asia along with their ability to cause direct infection in mammals and humans, raises public health concerns. H9N2 AI was reported for the first time in Iran in 1998 and at present it is endemic in poultry. This study was carried out to evaluate the exposure to H9N2 AI viruses among poultry workers from the Fars province. METHODS: 100 poultry workers and 100 healthy individuals with no professional exposure to poultry took part in this study. Serum samples were tested for antibodies against two distinct H9N2 avian influenza viruses, which showed different phylogenetic clustering and important molecular differences, such as at the amino acid (aa) position 226 (Q/L) (H3 numbering), using haemagglutination inhibition (HI) and microneutralization (MN) assays. RESULTS: Results showed that 17 % of the poultry workers were positive for the A/chicken/Iran/10VIR/854-5/2008 virus in MN test and 12 % in HI test using the titer ≥40 as positive cut-off value. Only 2 % of the poultry workers were positive for the A/chicken/Iran/12VIR/9630/1998 virus. Seroprevalence of non exposed individuals for both H9N2 strains was below 3 % by both tests. Statistical analyses models showed that exposure to poultry significantly increases the risk of infection with H9N2 virus. CONCLUSIONS: The results have demonstrated that exposure to avian H9N2 viruses had occurred among poultry workers in the Fars province of Iran. Continuous surveillance programmes should be implemented to monitor the presence of avian influenza infections in humans and to evaluate their potential threat to poultry workers and public health.

Hepatitis E virus genotype 4 in a pig farm, Italy, 2013.

Zoonotic strains of hepatitis E virus (HEV) in Europe have been reported to belong to genotypes 3 and 4. In 2012 and 2013, 57 pig farms in Northern Italy that had previously resulted seropositive for HEV were surveyed for the presence of the virus, with positive samples subsequently genotyped. Hepatitis E RNA was identified in 17/57 (29·8%) seropositive farms. Phylogenetic analysis demonstrated that distinct subtypes of genotype 3 were circulating in the north-east of Italy; as well, for the first time in the Italian swine population, genotype 4 was identified and attributed to subtype d.

Antigenic and genetic analyses of isolate APMV/wigeon/Italy/3920-1/2005 indicate that it represents a new avian paramyxovirus (APMV-12).

Isolate wigeon/Italy/3920-1/2005 (3920-1) was obtained during surveillance of wild birds in November 2005 in the Rovigo province of Northern Italy and shown to be a paramyxovirus. Analysis of cross-haemagglutination-inhibition tests between 3920-1 and representative avian paramyxoviruses showed only a low-level relationship to APMV-1. Phylogenetic analysis of the whole genome and each of the six genes indicated that while 3920-1 grouped with APMV-1 and APMV-9 viruses, it was quite distinct from these two. In the whole-genome analysis, 3920-1 had 52.1 % nucleotide sequence identity to the closest APMV-1 virus, 50.1 % identity to the APMV-9 genome, and less than 42 % identity to representatives of the other avian paramyxovirus groups. We propose isolate wigeon/Italy/3920-1/2005 as the prototype strain of a further APMV group, APMV-12.

Epidemiology and control of low pathogenicity avian influenza infections in rural poultry in Italy.

We analyzed the involvement of the rural poultry sector in outbreaks of low pathogenicity avian influenza (AI) in Italy in 2007-2009 and discuss possible measures for improving monitoring and control. A description of how the rural poultry sector is organized also is provided. Data were obtained by the AI surveillance system established in the areas affected by the outbreaks. The surveillance activities identified two H7N3 epidemics, in 2007 and 2009, both of which mainly involved the rural sector, yet these activities did not allow for the prompt eradication of the disease. Additional strategies could be adopted to avoid the persistence of AI within the rural sector, based on the regulation and control of poultry holdings at the top of the production chain.

The central role of Italy in the spatial spread of USUTU virus in Europe.

USUTU virus (USUV) is an arbovirus maintained in the environment through a bird-mosquito enzootic cycle. Previous surveillance plans highlighted the endemicity of USUV in North-eastern Italy. In this work, we sequenced 138 new USUV full genomes from mosquito pools (Culex pipiens) and wild birds collected in North-eastern Italy and we investigated the evolutionary processes (phylogenetic analysis, selection pressure and evolutionary time-scale analysis) and spatial spread of USUV strains circulating in the European context and in Italy, with a particular focus on North-eastern Italy. Our results confirmed the circulation of viruses belonging to four different lineages in Italy (EU1, EU2, EU3 and EU4), with the newly sequenced viruses from the North-eastern regions, Veneto and Friuli Venezia Giulia, belonging to the EU2 lineage and clustering into two different sub-lineages, EU2-A and EU2-B. Specific mutations characterize each European lineage and geographic location seem to have shaped their phylogenetic structure. By investigating the spatial spread in Europe, we were able to show that Italy acted mainly as donor of USUV to neighbouring countries. At a national level, we identified two geographical clusters mainly circulating in Northern and North-western Italy, spreading both northward and southward. Our analyses provide important information on the spatial and evolutionary dynamics of USUTU virus that can help to improve surveillance plans and control strategies for this virus of increasing concern for human health.

Author Correction: Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Unrevealed genetic diversity of GII Norovirus in the swine population of North East Italy.

Noroviruses (NoVs) are one of the major causative agents of non-bacterial gastroenteritis in humans worldwide. NoVs, belonging to Caliciviridae, are classified into ten genogroups (G) and eight P-groups based on major capsid protein (VP1) and of the RNA-dependent-RNA-polymerase (RdRp), respectively. In swine, the main genogroup and P-group identified are GII and GII.P; which can infect humans too. To date, only one case of GIIP.11 have been identified in swine in Italy while the circulation of other P-types is currently unknown. In the present study, 225 swine faecal samples were collected from 74 swine herds in Veneto region through on-farm monitoring. NoV circulation was particularly high in older pigs. The phylogenetic analysis showed the co-circulation of NoVs belonging to two different P-types: GII.P11 and GII.P18, here described for the first time in Italy, presenting an extensive genetic diversity, never described before worldwide. Distinct NoV genetic subgroups and unique amino acid mutations were identified for each P-type for the first time. This study demonstrated the co-circulation of diverse swine NoVs subgroups in Italy, raising questions on the origin of such diversity and suggesting that continuous monitoring of swine NoVs is needed to track the emergence of potentially zoonotic viruses by recombination events.

Nearly Complete Genome Sequence of a Sapelovirus A Strain Identified in Swine in Italy.

We report the first nearly complete genome sequence of a porcine sapelovirus (PSV) A strain that was identified from feces of piglets suffering from diarrhea in Italy in 2015. Phylogenetic investigations revealed a separate clustering for the Italian PSV, indicating unique molecular features.

Identification of a zoonotic genotype 3 hepatitis E subtype in wildlife in north-eastern Italy.

Hepatitis E virus (HEV) is an emerging zoonosis caused by a positive RNA single stranded virus of the Hepeviridae family. In developed countries, pigs and wild boars are the main reservoir for zoonotic genotypes 3 and 4. In spring 2017, for the first time HEV was detected in wild boars captured in the Regional Park of the Euganean Hills, in north-eastern Italy. Phylogenetic analysis of two complete viral genomes and seven partial ORF1 and ORF2 sequences of HEV viruses, selected from twelve positive animals, showed that the viruses grouped together within genotype 3 but clustered separately from previously identified subtypes, thus suggesting the identification of a novel genotype 3 subtype. The phylogenetic analysis of nine partial ORF2 sequences showed the closest similarity with wild boar/human viruses identified in central-northern Italy in 2012. The circulation of HEVs in this area, characterized by a vast man-made environment, an overpopulation of wild boars and >150 swine farms, should be considered in a public health perspective. Further investigations at the wild/domestic species and human interface are therefore necessary to gain a deeper understanding of HEV dynamics.

Integration of genetic and epidemiological data to infer H5N8 HPAI virus transmission dynamics during the 2016-2017 epidemic in Italy.

Between October 2016 and December 2017, several European Countries had been involved in a massive Highly Pathogenic Avian Influenza (HPAI) epidemic sustained by H5N8 subtype virus. Starting on December 2016, also Italy was affected by H5N8 HPAI virus, with cases occurring in two epidemic waves: the first between December 2016 and May 2017, and the second in July-December 2017. Eighty-three outbreaks were recorded in poultry, 67 of which (80.72%) occurring in the second wave. A total of 14 cases were reported in wild birds. Epidemiological information and genetic analyses were conjointly used to get insight on the spread dynamics. Analyses indicated multiple introductions from wild birds to the poultry sector in the first epidemic wave, and noteworthy lateral spread from October 2017 in a limited geographical area with high poultry densities. Turkeys, layers and backyards were the mainly affected types of poultry production. Two genetic sub-groups were detected in the second wave in non-overlapping geographical areas, leading to speculate on the involvement of different wild bird populations. The integration of epidemiological data and genetic analyses allowed to unravel the transmission dynamics of H5N8 virus in Italy, and could be exploited to timely support in implementing tailored control measures.

H7N7 Highly Pathogenic Avian Influenza in Poultry Farms in Italy in 2016.

After the H7N7 highly pathogenic (HP) avian influenza (AI) outbreak in 2013, and a single case of H5N8 HPAI in 2014, in April 2016, a H7N7 HPAI virus was detected in northeastern Italy. The case occurred in an organic free-range laying hen farm located in proximity with one of the highest densely populated poultry areas (DPPAs) in Italy. Control measures provided by the Council of the European Union in directive 2005/94/CE were promptly applied, and enhanced surveillance activities were implemented in the DPPAs. On May 16, 2016, a second case was confirmed in a fattening turkey farm within the protection zone of the previous outbreak. Following an epidemiologic inquiry, another turkey farm was considered at risk of transmission and was subjected to preemptive culling. Epidemiologic data and phylogenetic analyses indicated that the virus was likely introduced from wild birds as a low pathogenicity AI strain, through direct contact. The rapid containment of the outbreak proves the level of preparedness of the veterinary public health sector in Italy. Nevertheless, the recurrent introductions from wild birds indicate the need of improving both the biosecurity levels in the DPPA and the surveillance activities in wild birds to quickly detect the presence of AI in the territory.

Urgent request on avian influenza.

Highly pathogenic avian influenza (HPAI) H5N8 is currently causing an epizootic in Europe, infecting many poultry holdings as well as captive and wild bird species in more than 10 countries. Given the clear clinical manifestation, passive surveillance is considered the most effective means of detecting infected wild and domestic birds. Testing samples from new species and non-previously reported areas is key to determine the geographic spread of HPAIV H5N8 2016 in wild birds. Testing limited numbers of dead wild birds in previously reported areas is useful when it is relevant to know whether the virus is still present in the area or not, e.g. before restrictive measures in poultry are to be lifted. To prevent introduction of HPAIV from wild birds into poultry, strict biosecurity implemented and maintained by the poultry farmers is the most important measure. Providing holding-specific biosecurity guidance is strongly recommended as it is expected to have a high impact on the achieved biosecurity level of the holding. This is preferably done during peace time to increase preparedness for future outbreaks. The location and size of control and in particular monitoring areas for poultry associated with positive wild bird findings are best based on knowledge of the wider habitat and flight distance of the affected wild bird species. It is recommended to increase awareness among poultry farmers in these established areas in order to enhance passive surveillance and to implement enhanced biosecurity measures including poultry confinement. There is no scientific evidence suggesting a different effectiveness of the protection measures on the introduction into poultry holdings and subsequent spread of HPAIV when applied to H5N8, H5N1 or other notifiable HPAI viruses.

Emergence of a new genetic lineage of Newcastle disease virus in West and Central Africa--implications for diagnosis and control.

Newcastle disease (ND) is an OIE listed disease caused by virulent avian paramyxovirus type 1 (APMV-1) strains, which affect many species of birds and may cause severe economic losses in the poultry sector. The disease has been officially and unofficially reported in many African countries and still remains the main poultry disease in commercial and rural chickens of Africa. Unfortunately, virological and epidemiological information concerning ND strains circulating in the Western and Central regions of Africa is extremely scarce. In the present study, sequence analysis, pathotyping and detailed genetic characterization of virulent ND strains detected in rural poultry in West and Central Africa revealed the circulation of a new genetic lineage, distinguishable from the lineages described in the Eastern and Southern parts of the continent. Several mismatches were observed in the segment of the matrix gene targeted by the primers and probe designed for the molecular detection of APMV-1, which were responsible for the false negative results in the diagnostic test conducted. Furthermore, deduced amino acid sequences of the two major antigens eliciting a protective immune response (F and HN glycoprotein) revealed protein similarities <90% if compared to some common vaccine strains. Distinct mutations located in the neutralizing epitopes were revealed, indicating the need for detailed assessment of the efficacy of the current vaccines and vaccination practices in Africa. The present investigation provides important information on the epidemiology, diagnosis and control of NDV in Africa and highlights the importance of supporting surveillance in developing countries for transboundary animal diseases.