Re-emergence of Bagaza virus in wild birds from southern Spain

Bagaza virus (BAGV; Orthoflavivirus bagazaense) is an emerging vector-borne flavivirus affecting avian species with severe implications for animal health, and whose zoonotic potential has also been suggested. The aim of the present study was to monitor the epidemic outbreak of BAGV in wild birds from Spain in 2021. BAGV cases were confirmed in game bird species, including red-legged partridges (Alectoris rufa) and common pheasants (Phasianus colchicus) from 24 hunting areas. Suspected cases (clinical signs and/or mortality compatible with BAGV infection but without molecular confirmation) were also detected in 11 additional hunting areas. The outbreaks showed a seasonality mainly restricted to July and August. Estimated morbidity [25.8 % (95 %CI: 11.3-40.3) in partridges and 8.7 % (95 %CI: 0.0-18.0) in pheasants] and mortality rates [27.3 % (95 %CI: 12.5-42.1) in partridges and 13.0 % (95 %CI: 1.9-24.1) in pheasants] were found in the affected hunting areas. In addition, 215 non-game birds belonging to 46 different species were sampled by passive surveillance upon admittance to rehabilitation centres during 2021. BAGV infection was detected for the first time in green woodpecker (Picus viridis), spoonbill (Platalea leucorodia), white stork (Ciconia ciconia) and cynereous vulture (Aegypius monachus), expanding the host range of this emerging pathogen. In contrast to other species, game birds showed distinct BAGV related lesions, primarily myocarditis and encephalitis in addition to inflammatory infiltrates and necrosis in the liver and kidney. Molecular analyses revealed a homology of 97.4-98.0 % and 92.5-92.7 % between the BAGV sequences obtained in the present study (492 bp) and those isolated in 2010 and 2019 in southern Spain, respectively. These results allow to hypothesise about the likely silent and endemic circulation of BAGV since 2010 in this European region, although repeated virus reintroduction from neighbouring territories cannot be ruled out. Our findings evidence the sanitary, ecological and conservation implications of the re-emerged BAGV for wild birds, also emphasising the need to increase surveillance for monitoring and early detection of flavivirus dynamics in high-risk areas.

Emergence of Two Different Genotypes of Bagaza Virus (BAGV) Affecting Red-Legged Partridges in Spain, in 2019 and 2021

Bagaza virus (BAGV) is a flavivirus that affects avian species. In Europe, it was detected for the first time in Spain in 2010, exhibiting high genetic relatedness to Israel turkey meningoencephalomyelitis virus (ITMV) isolates from Israel. After a period of epidemiological silence, BAGV re-emerged, causing important outbreaks in 2019 and 2021. This study aims to characterize the newly detected strains and to elucidate if these recent outbreaks were caused by single or different virus introductions into the country. Hence, Spanish BAGV isolates from 2019 (n = 3) and 2021 (n = 1) outbreaks, obtained from red-legged partridges in Cádiz, were sequenced and further characterized. The phylogenetic analyses showed that they belong to two different genotypes: BAGV-Genotypes 1 and 2. Isolates from 2019 belong to BAGV-Genotype 1, closely related to isolates from Senegal, where BAGV has been circulating for decades. In turn, the 2021 isolates belong to BAGV-Genotype 2, closely related to those detected in Spain in 2010. Additionally, the comparison of the viral polyproteins of several BAGV isolates from both genotypes supports and confirms the phylogenetic findings. To conclude, BAGV has been introduced into Spain on at least three independent occasions, with alternating genetic clades, thus confirming that BAGV is able to sporadically reach Southern Europe.

Genome Characterization and Spaciotemporal Dispersal Analysis of Bagaza Virus Detected in Portugal, 2021

In September 2021, Bagaza virus (BAGV), a member of the Ntaya group from the Flavivirus genus, was detected for the first time in Portugal, in the heart and the brain of a red-legged partridge found dead in a hunting ground in Serpa (Alentejo region; southern Portugal). Here we report the genomic characterization of the full-length sequence of the BAGV detected (BAGV/PT/2021), including phylogenetic reconstructions and spaciotemporal analyses. Phylogenies inferred from nucleotide sequence alignments, complemented with the analysis of amino acid alignments, indicated that the BAGV strain from Portugal is closely related to BAGV strains previously detected in Spain, suggesting a common ancestor that seems to have arrived in the Iberia Peninsula in the late 1990s to early 2000s. In addition, our findings support previous observations that BAGV and Israel turkey meningoencephalitis virus (ITV) belong to the same viral species.

Bagaza Virus in Wild Birds, Portugal, 2021

Bagaza virus emerged in Spain in 2010 and was not reported in other countries in Europe until 2021, when the virus was detected by molecular methods in a corn bunting and several red-legged partridges in Portugal. Sequencing revealed high similarity between the 2021 strains from Portugal and the 2010 strains from Spain.

A Duplex Quantitative Real-Time Reverse Transcription-PCR for Simultaneous Detection and Differentiation of Flaviviruses of the Japanese Encephalitis and Ntaya Serocomplexes in Birds

High impact, mosquito-borne flaviviruses such as West Nile virus (WNV), Usutu virus (USUV), Japanese encephalitis virus (JEV), Tembusu virus (TMUV), and Bagaza/Israel turkey meningoencephalomyelitis virus (BAGV/ITV) are emerging in different areas of the world. These viruses belong to the Japanese encephalitis (JE) serocomplex (JEV, WNV, and USUV) and the Ntaya serocomplex (TMUV and BAGV/ITV). Notably, they share transmission route (mosquito bite) and reservoir host type (wild birds), and some of them co-circulate in the same areas, infecting overlapping mosquito and avian population. This may simplify epidemiological surveillance, since it allows the detection of different infections targeting the same population, but also represents a challenge, as the diagnostic tools applied need to detect the whole range of flaviviruses surveyed, and correctly differentiate between these closely related pathogens. To this aim, a duplex real-time RT-PCR (dRRT-PCR) method has been developed for the simultaneous and differential detection of JE and Ntaya flavivirus serocomplexes. The method has been standardized and evaluated by analyzing a panel of 49 flaviviral and non-flaviviral isolates, and clinical samples of different bird species obtained from experimental infections or from the field, proving its value for virus detection in apparently healthy or suspicious animals. This new dRRT-PCR technique is a reliable, specific and highly sensitive tool for rapid detection and differentiation of JE and Ntaya flavivirus groups in either domestic or wild animals. This novel method can be implemented in animal virology diagnostic laboratories as screening tool in routine surveillance and in the event of bird encephalitis emergence.

Influence of flavivirus co-circulation in serological diagnostics and surveillance: A model of study using West Nile, Usutu and Bagaza viruses

This study aims at assessing the serological cross-reactions existing between three mosquito-borne flaviviruses with avian reservoirs co-circulating in Europe: West Nile (WNV), Usutu (USUV) and Bagaza (BAGV). The study is useful for a better interpretation of serological results in diagnostics and surveillance. Serum samples obtained from a natural host, the red-legged partridge (Alectoris rufa), experimentally infected with WNV, USUV or BAGV were analysed using two commercially available WNV competition ELISAs suitable for serological surveillance, and by the confirmatory virus neutralization test (VNT). The ELISAs examined showed different levels of specificity for WNV, as judged by cross-reaction observed with the other flaviviruses. By VNT, virus-specific antibodies were confirmed in 80%, 50% or 0% of sera from WNV-, BAGV-, or USUV-inoculated birds, respectively. The results indicate how the co-circulation of cross-reacting flaviviruses may affect the outcomes of WNV serological surveillance when applying currently available serological tools. On the one hand, the choice of the ELISA test for antibody screening should consider the differences found in specificity, since one test is more specific for WNV while the other one is more suitable for detection of a broader range of flavivirus antibodies. On the other hand, besides corroborating that cross-neutralization occurs between flaviviruses from different serocomplexes (WNV/USUV and BAGV), this study points out that cross-neutralization between WNV and USUV is not symmetric, and reveals the difficulty to identify USUV infections serologically. This finding indicates that actual USUV infections might be underestimated in the current diagnostic schemes.

Experimental infection of grey partridges with Bagaza virus: pathogenicity evaluation and potential role as a competent host

Bagaza virus (BAGV; synonymous to Israel turkey meningoencephalomyelitis virus, ITV) is a relevant arthropod-borne epornitic flavivirus. In its first emergence in Europe (southern Spain, 2010) BAGV caused an outbreak, severely affecting red-legged partridges and common pheasants. The effects (pathogenicity, role as reservoir host) of BAGV in other European phasianids are unknown. To fill this gap, grey partridges were experimentally infected with BAGV. The clinical course of the disease was severe, with neurological signs, significant weight loss and 40% mortality. Low viral loads in the blood and the absence of contact transmission suggest a limited—if any—role on BAGV transmission for this European phasianid.

A one-step TaqMan real-time qRT-PCR assay for the specific detection and quantitation of the Spanish goat encephalitis virus (SGEV)

Louping ill-like virus (LI) has been recently detected in two different locations in the north of Spain and separated by only around 400 km. Using molecular approaches, the viruses causing both outbreaks have been shown to be different to LI virus, but also different to each other. They have been called SSEV (Spanish sheep encephalitis virus) and SGEV (Spanish goat encephalitis virus) taking into account the species from which they were isolated. The aim of this paper was to design a quantitative TaqMan real-time RT-PCR protocol, for the specific diagnostic and quantitation of SGEV. Linearity, efficiency and dynamic range as well as reproducibility and specificity of the method has been tested and established. The method has proved to be valid for the specific detection and viral load quantitation of SGEV genome in virus isolates and tissue samples from infected animals. This assay will be a useful analytical tool in early diagnosis and epidemiological surveys.

Bagaza virus is pathogenic and transmitted by direct contact in experimentally infected partridges, but is not infectious in house sparrows and adult mice

Bagaza virus (BAGV) is a mosquito-borne flavivirus belonging to the Ntaya serocomplex. In 2010, a disease outbreak was reported in Cádiz (Southern Spain) affecting game birds (red-legged partridges and common pheasants). In this work, red-legged partridges were inoculated experimentally with infectious BAGV isolated from this outbreak in order to make a complete clinical and analytical assessment of the disease caused by the pathogen in this species. Viral load (by real-time RT-PCR) in blood, oral and cloacal swabs, and feathers, and neutralizing antibody titres (by VNT) were measured. In order to determine direct contact transmission, non-inoculated partridges were caged together with the inoculated ones. To assess infectiousness in other species, house sparrows and mice were also inoculated with the virus. All the inoculated partridges were clinically affected, and 30% of them died. All the infected individuals lost weight, with larger losses being recorded in females. Conversely, no mortality or disease symptoms were observed in the sparrows or mice. Remarkably, all the contact partridges acquired the infection by direct (non-vectored) transmission. This study confirms that the red-legged partridge is a susceptible host for BAGV infection, and that this pathogen is transmitted by direct contact. Long-lasting viral loads detected in calami of immature feathers demonstrate that feather sampling could be a useful strategy in active surveillance programs for early detection of BAGV.

Bagaza virus and Israel turkey meningoencephalomyelitis virus are a single virus species

Bagaza virus (BAGV) and Israel turkey meningoencephalomyelitis virus (ITV) are classified in the genus Flavivirus of the family Flaviviridae. Serologically, they are closely related, belonging to the Ntaya serocomplex. Nucleotide sequences available to date consist of several complete sequences of BAGV isolates, but only partial sequences of ITV isolates. Sequence comparisons of partial envelope (E) and NS5 regions reveal a close genetic relationship between these viruses. Despite this, BAGV and ITV are considered as separate virus species in the database of the International Committee on Taxonomy of Viruses. In this work, complete nucleotide sequences for five ITV isolates are provided, thereby permitting a phylogenetic comparison with other complete sequences of flaviviruses in the Ntaya serogroup. We conclude that BAGV and ITV are the same virus species and propose that both viruses be designated by a new unified name: Avian meningoencephalomyelitis virus.

A novel quantitative multiplex real-time RT-PCR for the simultaneous detection and differentiation of West Nile virus lineages 1 and 2, and of Usutu virus

An increase in activity of two mosquito-borne flaviviruses, West Nile virus (WNV) and Usutu virus (USUV), has been reported in Europe in recent years. The current epidemiological situation calls for RT-PCR methods that are able to detect not only the widespread lineage 1 (L1) WNV, but also lineage 2 (L2) WNV. In addition, the presence in Europe of the closely related USUV requires methods that can identify these three flaviviruses and permit an efficient and accurate differential diagnosis. Here we describe a new one-step real-time multiplex RT-PCR that detects and differentiates efficiently WNV-L1, WNV-L2 and USUV in a single reaction. The assay is based on different sets of primers and fluorogenic probes specific to each virus that are labelled with selective, non-overlapping fluorogen-quencher pairs. This enables the fluorescence emitted by each probe, characterized by distinct wavelengths, to be differentiated. This multiplex assay was very sensitive to all of the target viruses; in addition, there were no cross-reactions between the viruses and the assay did not react to any other phylogenetically or symptomatically related viruses. Quantitation was enabled through the use of in vitro-transcribed RNAs developed specifically for each virus as copy number standards. This new assay was validated using different types of experimental and field samples.