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1.
Viruses ; 13(8)2021 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-34452311

RESUMEN

Since 2006, multiple outbreaks of avian influenza (AI) have been reported in Nigeria involving different subtypes. Surveillance and molecular epidemiology have revealed the vital role of live bird markets (LBMs) in the dissemination of AI virus to commercial poultry farms. To better understand the ecology and epidemiology of AI in Nigeria, we performed whole-genome sequencing of nineteen H9N2 viruses recovered, from apparently healthy poultry species, during active surveillance conducted in nine LBMs across Nigeria in 2019. Analyses of the HA gene segment of these viruses showed that the H9N2 strains belong to the G1 lineage, which has zoonotic potential, and are clustered with contemporary H9N2 identified in Africa between 2016 and 2020. We observed two distinct clusters of H9N2 viruses in Nigeria, suggesting different introductions into the country. In view of the zoonotic potential of H9N2 and the co-circulation of multiple subtypes of AI virus in Nigeria, continuous monitoring of the LBMs across the country and molecular characterization of AIVs identified is advocated to mitigate economic losses and public health threats.

2.
Transbound Emerg Dis ; 2021 Jan 21.
Artículo en Inglés | MEDLINE | ID: mdl-33480188

RESUMEN

Among recurrent sanitary emergencies able to spread rapidly worldwide, avian influenza is one of the main constraints for animal health and food security. In West Africa, Nigeria has been experiencing repeated outbreaks of different strains of avian influenza virus (AIV) since 2006 and is also recognized as a hot spot in the region for the introduction of emerging strains by migratory wild birds. Here, we generated complete genomes of 20 highly pathogenic avian influenza (HPAI) H5N8 viruses collected during active surveillance in Nigerian live bird markets (LBM) and from outbreaks reported in the country between 2016 and 2019. Phylogenetic analysis reveals that the Nigerian viruses cluster into four separate genetic groups within HPAI H5 clade 2.3.4.4b. The first group includes 2016-2017 Nigerian viruses with high genetic similarity to H5N8 viruses detected in Central African countries, while the second includes Nigerian viruses collected both in LBM and poultry farms (2018-2019), as well as in Cameroon, Egypt and Siberia. A natural reassortant strain identified in 2019 represents the third group: H5N8 viruses with the same gene constellation were identified in 2018 in South Africa. Finally, the fourth introduction represents the first detection in the African continent of the H5N6 subtype, which is related to European viruses. Bayesian phylogeographic analyses confirmed that the four introductions originated from different sources and provide evidence of the virus spread within Nigeria, as well as diffusion beyond its borders. The multiple epidemiological links between Nigeria, Central and Southern African countries highlight the need for harmonized and coordinated surveillance system to control AIV impact. Improved surveillance at the Wetlands, LBMs and early warning of outbreaks are crucial for prevention and control of AIV, which can be potentially zoonotic and be a threat to human health.

3.
Transbound Emerg Dis ; 68(1): 152-167, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-32613724

RESUMEN

Comprehensive understanding of the patterns and drivers of avian influenza outbreaks is pivotal to inform surveillance systems and heighten nations' ability to quickly detect and respond to the emergence of novel viruses. Starting in early 2017, the Italian poultry sector has been involved in the massive H5N8 highly pathogenic avian influenza epidemic that spread in the majority of the European countries in 2016/2017. Eighty-three outbreaks were recorded in north-eastern Italy, where a densely populated poultry area stretches along the Lombardy, Emilia-Romagna and Veneto regions. The confirmed cases, affecting both the rural and industrial sectors, depicted two distinct epidemic waves. We adopted a combination of multivariate statistics techniques and multi-model regression selection and inference, to investigate how environmental factors relate to the pattern of outbreaks diversity with respect to their spatiotemporal and genetic diversity. Results showed that a combination of eco-climatic and host density predictors were associated with the outbreaks pattern, and variation along gradients was noticeable among genetically and geographically distinct groups of avian influenza cases. These regional contrasts may be indicative of a different mechanism driving the introduction and spreading routes of the influenza virus in the domestic poultry population. This methodological approach may be extended to different spatiotemporal scale to foster site-specific, ecologically informed risk mitigating strategies.


Asunto(s)
Brotes de Enfermedades/veterinaria , Subtipo H5N8 del Virus de la Influenza A/fisiología , Gripe Aviar/epidemiología , Enfermedades de las Aves de Corral/epidemiología , Animales , Pollos , Patos , Gansos , Variación Genética , Subtipo H5N8 del Virus de la Influenza A/genética , Gripe Aviar/virología , Italia/epidemiología , Enfermedades de las Aves de Corral/virología , Análisis Espacio-Temporal , Pavos
4.
Transbound Emerg Dis ; 68(1): 37-50, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31788978

RESUMEN

Effective control of avian diseases in domestic populations requires understanding of the transmission dynamics facilitating viral emergence and spread. In 2016-17, Italy experienced a significant avian influenza epidemic caused by a highly pathogenic A(H5N8) virus, which affected domestic premises housing around 2.7 million birds, primarily in the north-eastern regions with the highest density of poultry farms (Lombardy, Emilia-Romagna and Veneto). We perform integrated analyses of genetic, spatiotemporal and host data within a Bayesian phylogenetic framework. Using continuous and discrete phylogeography, we estimate the locations of movements responsible for the spread and persistence of the epidemic. The information derived from these analyses on rates of transmission between regions through time can be used to assess the success of control measures. Using an approach based on phylogenetic-temporal distances between domestic cases, we infer the presence of cryptic wild bird-mediated transmission, information that can be used to complement existing epidemiological methods for distinguishing transmission within the domestic population from incursions across the wildlife-domestic interface, a common challenge in veterinary epidemiology. Spatiotemporal reconstruction of the epidemic reveals a highly skewed distribution of virus movements with a high proportion of shorter distance local movements interspersed with occasional long-distance dispersal events associated with wild birds. We also show how such inference be used to identify possible instances of human-mediated movements where distances between phylogenetically linked domestic cases are unusually high.


Asunto(s)
Pollos , Patos , Epidemias/veterinaria , Subtipo H5N8 del Virus de la Influenza A/fisiología , Gripe Aviar/transmisión , Enfermedades de las Aves de Corral/transmisión , Pavos , Animales , Teorema de Bayes , Gripe Aviar/epidemiología , Gripe Aviar/virología , Italia/epidemiología , Filogenia , Enfermedades de las Aves de Corral/epidemiología , Enfermedades de las Aves de Corral/virología , Análisis Espacio-Temporal
5.
EFSA J ; 18(11): e06341, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-33281979

RESUMEN

Since 16 October 2020, outbreaks ofhighly pathogenic avian influenza (HPAI) viruseshavebeen reported inseveral EU/EEAcountries -Belgium, Denmark, France, Germany, Ireland, the Netherlands, and Swedenas well asin the United Kingdom.As of 19 November,12pm, 302 HPAI A(H5) detections have been reported, with the majority of the detections referring to wild birds (n=281), and a few related to outbreaks in poultry (n=18) and captive birds (n=3). Most of the detections in wild birds were in wild waterbirds,being barnacle goose the most affected species (n=110), followed by greylag goose (n=47), Eurasian wigeon (n=32),mallard (n=14), and common buzzard (n=13).ThreeHPAI virus subtypes were identified, A(H5N8), A(H5N5) and A(H5N1), with A(H5N8) being the most reported subtype (n=284). Phylogenetic analysis indicated that the viruses evolved from a single progenitor virus thatwent through multiple reassortment events. Based on the ongoing autumn migration of wild waterbirds to their wintering areas in Europe, there is a continued risk of further introduction of HPAI A(H5) viruses into Europe. Furthermore, given the expected movements of both migratory, and resident wild birds in Europe during winter, there is a high risk of further spread of HPAI A(H5) viruses within Europe. No genetic markers indicating adaptation to mammals have been identified in the viruses analysed so far,andno human infection due to avian influenza viruses detected in the recent outbreakshas been reported. For that reason,the risk to the general population remains very low.However,following the precautionary principle, people should avoid touching sick or dead birds unprotected to minimise any potential risk.

6.
EFSA J ; 18(9): e06270, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-33281980

RESUMEN

Between 16 May and 15 August 2020, seven highly pathogenic avian influenza (HPAI) A(H5N8) virus outbreaks were reported in Europe in poultry, with one outbreak reported in Bulgaria(n=1) andsix in Hungary (n=6) and one low pathogenic avian influenza (LPAI) A(H5N3) virus outbreak was reported in poultry in Italy. All six outbreaks detected in Hungary were secondary outbreaks and seem to be the tail end of the HPAI A(H5N8) epidemic that wasobserved in poultry over the winter and spring in central Europe from December 2019 (n=334).Genetic analysis of the HPAI A(H5N8) viruses isolated during this reporting period from Bulgaria and Hungary did not identify any major changes compared tothe viruses collected in the respective countries during the first months of 2020. This suggests a persistence of the virus in the two countries rather than new introductions via infectedwild birds. HPAI A(H5N8) virus has been detected in poultry and wild birds in western Russia within the reporting period, and as of the middle of September also in Kazakhstan. The presence of HPAI virus in western Russiaand in north Kazakhstan,spatially associated with autumnmigration routes of wild waterbirds, is of concern due to the possible spread of the virus via wild birds migrating to the EU.It is highly recommended thatMember States take appropriate measures to promptly detect suspected cases of HPAI, including increasing biosecurity measures. According to past experiences (2005-2006 and 2016-2017 epidemic waves), the northern and eastern European areas might be at higher risk of virus introduction in the coming autumn-winter seasonand should be the key regions where prompt response measures to early detect the virusshould be set up. One human case due to A(H9N2) avian influenza virus infection was reported during the reporting period.

7.
Vet Microbiol ; 248: 108820, 2020 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-32891950

RESUMEN

In December 2018, suspected outbreaks of equine influenza (EI) were observed in donkeys in Sokoto State, in the extreme northwest of Nigeria bordering the Republic of the Niger. Equine influenza virus (EIV) subtype H3N8 was the etiologic agent identified in the outbreaks using real-time RT-qPCR and sequencing of both the partial haemagglutinin (HA) gene and the complete genome. Since then the H3N8 virus spread to 7 of the 19 northern states of Nigeria, where it affected both donkeys and horses. Phylogenetic analysis of the partial and complete HA gene revealed the closest nucleotide similarity (99.7%) with EIVs belonging to the Florida clade 1 (Fc-1) of the American lineage isolated in 2018 from Argentina and Chile. In total, 80 amino acid substitutions were observed in the viral proteins when compared to the OIE-recommended Fc-1 vaccine strains. The HA and neuraminidase proteins respectively had 13 and 16 amino acid substitutions. This study represents the first reported outbreak of EI caused by an Fc-1 virus in Nigeria and in the West Africa sub-region. Based on this report, extensive disease surveillance in equids is required to establish the circulating lineages and design an effective control strategy to protect the considerable population of horses and donkeys in the country.

8.
EFSA J ; 18(3): e06096, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-32874270

RESUMEN

Between 16 November 2019 and 15 February 2020, 36 highly pathogenic avian influenza (HPAI) A(H5N8) virus outbreakswere reported in Europe in poultry (n=34), captive birds (n=1) and wild birds (n=2), in Poland, Hungary, Slovakia, Romania, Germany, Czechiaand Ukraine,one HPAI outbreakcaused by a simultaneous infection with A(H5N2) and A(H5N8) was reported in poultry in Bulgaria, andtwo low pathogenic avian influenza (LPAI) A(H5) virus outbreaks were reported in poultryin the United Kingdom and in Denmark. Genomic characterisation of the HPAI A(H5N8) viruses suggests that they are reassortants of HPAI A(H5N8) viruses from Africa and LPAI viruses from Eurasia. It is likely that this reassortment occurred in wild migratory birds in Asia during the summer and then spread to eastern Europe with the autumnmigration. This is the first time that wild bird migration from Africa to Eurasia has been implicated in the long-distance spread of HPAI viruses to the EU. Given the late incursion of HPAI A(H5N8) virus into the EU in this winter season (first outbreak reported on 30 December 2019), its overall restriction to eastern Europe, and the approaching spring migration, the risk of the virus spreadingfurther in the west via wild birds is decreasing for the coming months. Genetic analysis of the HPAI A(H5N2) and A(H5N8) viruses detected in the Bulgarian outbreak reveals that these virusesare both related to the 2018-19 Bulgarian HPAI A(H5N8) viruses and not to the HPAI A(H5N8) viruses currently circulating in Europe.An increasing number of HPAI A(H5N1), A(H5N2), A(H5N5) and A(H5N6) virus outbreaks in poultry in Asia were reported during the time period for this report compared with the previous reporting period. Single outbreaks of HPAI A(H5N8) virus were notified by Saudi Arabia and South Africa. Furthermore, in contrast to the last report, HPAI virus-positive wild birds were reported from Israel and one of the key migration areas in northern China.Two human cases due to A(H9N2) virus infection were reported during the reporting period.

9.
EFSA J ; 18(6): e06194, 2020 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-32874346

RESUMEN

Between 16 February and 15 May 2020, 290highly pathogenic avian influenza (HPAI) A(H5) virus outbreakswere reported in Europe in poultry (n=287), captive birds (n=2) and wild birds (n=1)in Bulgaria, Czechia,Germany,Hungary andPolandand two low pathogenic avian influenza (LPAI) A(H7N1) virus outbreaks were reported in poultry in Italy. 258 of 287 poultry outbreaks detected in Europe were secondary outbreaks, suggesting that in the large majoryty of cases the spread of the virus was not due to wild birds.Allthe HPAI outbreaks were A(H5N8) apart from three,which were reported as A(H5N2) from Bulgaria. Genetic analysis of the HPAI A(H5N8) viruses isolated from the eastern and central European countries indicates that this is a reassortant between HPAI A(H5N8) viruses from Africa and LPAI viruses from Eurasia. Two distict subtypes were identified in Bulgaria, a novel reassortant A(H5N2) and A(H5N8) that is persisting in the country since 2016. There could be several reasons why only very few HPAI cases were detected in wild birds in this 2019-2020 epidemic season and a better knowledge of wild bird movements and virus-host interaction (e.g. susceptibility of the hosts to this virus) could help to understand the reasons for poor detection of HPAI infected wild birds. In comparison with the last reporting period, a decreasing number of HPAI A(H5)-affected countries and outbreaks were reported from outside Europe. However, there is considerable uncertainty regarding the current epidemiological situation in many countries out of Europe. Four human cases due to A(H9N2) virus infection were reported during the reporting period from China.

10.
Emerg Infect Dis ; 26(7): 1557-1561, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32568059

RESUMEN

We report detection of a highly pathogenic avian influenza A(H5N8) clade 2.3.4.4b virus in Europe. This virus was generated by reassortment between H5N8 subtype virus from sub-Saharan Africa and low pathogenicity avian influenza viruses from Eurasia.


Asunto(s)
Subtipo H5N8 del Virus de la Influenza A , Gripe Aviar , África del Sur del Sahara/epidemiología , Animales , Europa (Continente) , Subtipo H5N8 del Virus de la Influenza A/genética , Gripe Aviar/epidemiología , Filogenia , Virus Reordenados/genética
11.
Front Microbiol ; 11: 1136, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32523585

RESUMEN

Bovine is considered the main reservoir of influenza D virus (IDV), however, low levels of seropositivity in other farmed species suggest a wide range of potential hosts. Nevertheless, it is not clear whether this scenario is the result of rare spillover events upon contact with bovines, or a lack of adaptation of IDV to these hosts. Among these species, sheep represents a crucial component of the rural economy in many developing countries, but little is known about its role in the ecology of the disease. To evaluate the susceptibility of sheep to IDV viruses of different origin, we used ovine respiratory tissues as an ex vivo model and investigated the infective phenotype of two IDV strains isolated from either bovine (IDV-BOV) or swine (IDV-SW). For translatability purposes, we included a parainfluenza type 3 virus, as positive control, given its known respiratory tropism in sheep. We performed a timed evaluation of the viral infectivity, cell tropism and the associated histopathology, by means of tissue culture infectious dose assays on supernatants and histological/immunohistochemical analyses on explanted tissues, respectively. To further investigate differences in the phenotype of these two strains and to identify the potential targets of replication in the most commonly land-based farmed mammalian species, we carried out virus binding assays on histological sections of the respiratory tract of bovine, caprine, ovine, horse and swine. Our results demonstrated that IDV successfully replicates in nasal, tracheal and lung ovine tissues, suggesting a moderate susceptibility of this species to IDV infection. Interestingly, despite the high genetic identity of these strains, IDV- BOV consistently replicated to higher titers than IDV-SW in all respiratory tracts, suggesting IDV viruses might display considerable levels of variability in their phenotype when crossing the species barrier. Virus binding assays confirmed a superior affinity of the IDV viruses for the bovine upper respiratory tract, and a preference for the pharyngeal epithelium of small ruminants, indicating possible targets to improve the sensitivity of virological sampling for diagnostic and post-mortem purposes. Further pathogenesis and cross-species transmission studies will be necessary to elucidate the ecology of IDV and eventually allow the design of cost-effective surveillance strategies.

12.
Transbound Emerg Dis ; 67(6): 2775-2788, 2020 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-32438523

RESUMEN

Avian coronaviruses, including infectious bronchitis virus (IBV) and turkey coronavirus (TCoV), are economically important viruses affecting poultry worldwide. IBV is responsible for causing severe losses to the commercial poultry sector globally. The objectives of this study were to identify the viruses that were causing outbreaks of severe respiratory disease in chickens in Trinidad and Tobago (T&T) and to characterize the strains. Swab samples were collected from birds showing severe respiratory signs in five farms on the island of Trinidad. Samples were tested for the presence of IBV, as well as avian influenza virus (AIV), Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) by real-time reverse transcription polymerase chain reaction (qRT-PCR). All samples from the five farms tested negative for AIV, NDV and aMPV; however, samples from clinically affected birds in all five of the farms tested positive for IBV. Genetic data revealed the presence of TCoV in chickens on two of the farms. Interestingly, these two farms had never reared turkeys. Phylogenetic analysis showed that IBV S1 sequences formed two distinct clusters. Two sequences grouped with vaccine strains within the GI-1 lineage, whereas three sequences grouped together, but separately from other defined lineages, forming a likely new lineage of IBV. Pairwise comparison revealed that the three unique variant strains within the distinct lineage of IBV were significantly different in their S1 nucleotide coding regions from viruses in the closest lineage (16% difference) and locally used vaccine strains (>20% difference). Results also suggested that one of the samples was a recombinant virus, generated from a recombination event between a Trinidad virus of the GI-1 lineage and a Trinidad virus of the newly defined lineage. Many amino acid differences were also observed between the S1 coding regions of the circulating field and vaccine strains, indicating that the IBV vaccines may not be protective. Vaccine-challenge studies are however needed to prove this.


Asunto(s)
Infecciones por Coronavirus/veterinaria , Virus de la Bronquitis Infecciosa/aislamiento & purificación , Enfermedades de las Aves de Corral/virología , Infecciones del Sistema Respiratorio/veterinaria , Vacunas Virales/inmunología , Animales , Pollos , Infecciones por Coronavirus/virología , Patos , Gansos , Virus de la Bronquitis Infecciosa/clasificación , Filogenia , Codorniz , ARN Viral , Infecciones del Sistema Respiratorio/virología , Análisis de Secuencia de ARN/veterinaria , Trinidad y Tobago , Pavos , Vacunación/veterinaria
13.
Infect Genet Evol ; 84: 104359, 2020 10.
Artículo en Inglés | MEDLINE | ID: mdl-32407794

RESUMEN

Canine distemper virus (CDV) represents an important threat for both wild and domestic carnivores. Since 2006, the North-Eastern regions in Italy have been experiencing severe and widespread recurring outbreaks of CDV affecting the wild carnivore population. In this study we performed an extensive phylogeographic analysis of CDV strains belonging to the Wildlife-Europe genetic group identified between 2006 and 2018 in Veneto, Trentino Alto Adige and Friuli Venezia Giulia regions. Our analysis revealed that viruses from the first (2006-2009) and the second (2011-2018) epidemic wave cluster separately, suggesting the introduction of two distinct genetic variants. These two events were characterized by different diffusion rates and spatial distribution, thus suggesting the existence of a connection between infection spread and host population dynamics. We also report the first spillover event of this strain to a non-vaccinated dog in a rural area of Friuli Venezia Giulia. The increasing prevalence of the infection in wildlife population, the broad host range of CDV circulating in the Alpine wildlife and the first reported transmission of a wild-adapted strain to a domestic dog in this region raise concerns over the vulnerability of wildlife species and the exposure of our pets to new threatening strains. Understanding the dynamic of CDV epidemics will also improve preparedness for re-emerging diseases affecting carnivore species.

14.
Emerg Microbes Infect ; 9(1): 851-854, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32403984

RESUMEN

A second case of a novel rabies variant described once in a capuchin monkey from Mato Grosso, Brazil, was discovered in a rabid wild kinkajou from the same region, indicating a public health risk following exposure to either of the two animals.


Asunto(s)
Cebus/virología , Procyonidae/virología , Virus de la Rabia/aislamiento & purificación , Rabia/transmisión , Animales , Brasil/epidemiología , Genes Virales , Filogenia , Salud Pública , Virus de la Rabia/genética
15.
Emerg Microbes Infect ; 9(1): 886-888, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32312185

RESUMEN

Since 2013, highly pathogenic avian influenza (HPAI) subtype H5N6 (clade 2.3.4.4) has been reported in wild birds and poultry in Asia as well as in other parts of the globe. In Africa, information on the presence of this virus subtype is lacking. This study reports the first detection of a HPAI (H5N6) virus (clade 2.3.4.4b) in a duck from a live bird market in Nigeria, whose genome is closely related to the European 2017-2018 H5N6 viruses, indricating a recent virus introduction into the African continent.


Asunto(s)
Animales Salvajes/virología , Virus de la Influenza A/aislamiento & purificación , Gripe Aviar/epidemiología , Filogenia , Enfermedades de las Aves de Corral/virología , Aves de Corral/virología , Animales , Brotes de Enfermedades/veterinaria , Patos/virología , Genoma Viral , Virus de la Influenza A/clasificación , Gripe Aviar/virología , Nigeria/epidemiología , Enfermedades de las Aves de Corral/epidemiología
16.
Infect Genet Evol ; 83: 104342, 2020 09.
Artículo en Inglés | MEDLINE | ID: mdl-32348876

RESUMEN

Since 2005, H5Nx highly pathogenic avian influenza (HPAI) viruses of the Goose/Guangdong (Gs/GD) lineage have spread worldwide, affecting poultry and wild birds in Asia, Europe, Africa and North America. So far, the role of Western Asia and the Middle East in the diffusion dynamics of this virus has been poorly explored. In order to investigate the genetic diversity and the role of Iran in the transmission dynamics of the Gs/GD lineage, we sequenced the complete genome of twenty-eight H5Nx viruses which were circulating in the country between 2016 and 2018. We reported the first characterization of the HPAI H5N6 subtype of clade 2.3.4.4B in Iran and gave evidence of the high propensity of the Gs/GD H5 AIVs to reassort, describing six novel H5N8 genotypes of clade 2.3.4.4B, some of them likely generated in this area, and one H5N1 reassortant virus of clade 2.3.2.1c. Our spatial analyses demonstrated that the viruses resulted from different viral introductions from Asia and Europe and provided evidence of virus spread from Iran to the Middle East. Therefore, Iran may represent a hot-spot for virus introduction, dissemination and for the generation of new genetic variability. Increasing surveillance efforts in this high-risk area is of utmost importance for the early detection of novel emerging strains with zoonotic potential.

17.
Bioinformatics ; 36(7): 2098-2104, 2020 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-31790143

RESUMEN

MOTIVATION: The potentially low precision associated with the geographic origin of sampled sequences represents an important limitation for spatially explicit (i.e. continuous) phylogeographic inference of fast-evolving pathogens such as RNA viruses. A substantial proportion of publicly available sequences is geo-referenced at broad spatial scale such as the administrative unit of origin, rather than more precise locations (e.g. geographic coordinates). Most frequently, such sequences are either discarded prior to continuous phylogeographic inference or arbitrarily assigned to the geographic coordinates of the centroid of their administrative area of origin for lack of a better alternative. RESULTS: We here implement and describe a new approach that allows to incorporate heterogeneous prior sampling probabilities over a geographic area. External data, such as outbreak locations, are used to specify these prior sampling probabilities over a collection of sub-polygons. We apply this new method to the analysis of highly pathogenic avian influenza H5N1 clade data in the Mekong region. Our method allows to properly include, in continuous phylogeographic analyses, H5N1 sequences that are only associated with large administrative areas of origin and assign them with more accurate locations. Finally, we use continuous phylogeographic reconstructions to analyse the dispersal dynamics of different H5N1 clades and investigate the impact of environmental factors on lineage dispersal velocities. AVAILABILITY AND IMPLEMENTATION: Our new method allowing heterogeneous sampling priors for continuous phylogeographic inference is implemented in the open-source multi-platform software package BEAST 1.10. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Subtipo H5N1 del Virus de la Influenza A , Gripe Aviar , Animales , Brotes de Enfermedades , Filogenia , Filogeografía , Probabilidad
18.
Viruses ; 11(12)2019 11 30.
Artículo en Inglés | MEDLINE | ID: mdl-31801277

RESUMEN

Influenza D virus (IDV) has been increasingly reported all over the world. Cattle are considered the major viral reservoir. Based on the hemagglutinin-esterase (HEF) gene, three main genetic and antigenic clusters have been identified: D/OK distributed worldwide, D/660 detected only in the USA and D/Japan in Japan. Up to 2017, all the Italian IDV isolates belonged to the D/OK genetic cluster. From January 2018 to May 2019, we performed virological surveillance for IDV from respiratory outbreaks in 725 bovine farms in Northern Italy by RT-PCR. Seventy-four farms were positive for IDV. A full or partial genome sequence was obtained from 29 samples. Unexpectedly, a phylogenetic analysis of the HEF gene showed the presence of 12 strains belonging to the D/660 cluster, previously unreported in Europe. The earliest D/660 strain was collected in March 2018 from cattle imported from France. Moreover, we detected one viral strain with a reassortant genetic pattern (PB2, PB1, P42, HEF and NP segments in the D/660 cluster, whilst P3 and NS segments in the D/OK cluster). These results confirm the circulation of IDV in the Italian cattle population and highlight the need to monitor the development of the spreading of this influenza virus in order to get more information about the epidemiology and the ecology of IDV viruses.


Asunto(s)
Enfermedades de los Bovinos/epidemiología , Brotes de Enfermedades/veterinaria , Infecciones por Orthomyxoviridae/veterinaria , Virus Reordenados , Thogotovirus/clasificación , Animales , Bovinos , Enfermedades de los Bovinos/virología , Geografía , Italia/epidemiología , Infecciones por Orthomyxoviridae/epidemiología , Infecciones por Orthomyxoviridae/virología , Filogenia , Prevalencia , Thogotovirus/genética , Thogotovirus/aislamiento & purificación
19.
Nat Commun ; 10(1): 5310, 2019 11 22.
Artículo en Inglés | MEDLINE | ID: mdl-31757953

RESUMEN

The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.


Asunto(s)
Gripe Aviar/transmisión , Gripe Humana/transmisión , Enfermedades de las Aves de Corral/transmisión , África , África Occidental , Animales , Humanos , Subtipo H5N1 del Virus de la Influenza A/genética , Subtipo H5N8 del Virus de la Influenza A/genética , Virus de la Influenza A/genética , Gripe Aviar/economía , Gripe Aviar/epidemiología , Gripe Aviar/virología , Gripe Humana/economía , Gripe Humana/epidemiología , Gripe Humana/virología , Filogenia , Aves de Corral , Enfermedades de las Aves de Corral/economía , Enfermedades de las Aves de Corral/epidemiología , Enfermedades de las Aves de Corral/virología
20.
Microbiol Resour Announc ; 8(41)2019 Oct 10.
Artículo en Inglés | MEDLINE | ID: mdl-31601657

RESUMEN

Rabbit endogenous lentivirus type K (RELIK) was discovered in the genome of the European rabbit (Oryctolagus cuniculus). In our study, we present three complete genome sequences of RELIK viruses generated using a target amplification approach performed on the RNA of commercial rabbits from Italy.

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