Background West Nile virus (WNV) is spreading rapidly to numerous countries in Europe. WNV maintains an enzootic cycle with many bird species as key amplifying hosts and mosquitoes of the Culex pipiens complex as main vectors. Worldwide, nine WNV lineages have been described so far. The objective of this study was to elucidate the genetic diversity of WNV in Germany in 2023 and 2024 with a focus on birds as reservoir hosts. Methods A total of 86 samples (25 from 2023, 61 from 2024) from dead and live birds submitted by German state veterinary laboratories and as part of a nationwide wild bird surveillance network. Samples were selected for whole genome sequencing (WGS) based on bird species, Ct value, and location. Viral RNA was extracted from bird samples and submitted to two WNV specific reverse transcription quantitative real-time polymerase chain reaction protocols. Subsequently, viral RNAs were amplified, WGS was performed using MinION technology and WGS data were processed to determine lineages and clusters. Results The majority of WNV RNA positive birds selected for WGS in 2023 and 2024 were Eurasian Goshawks ( Astur gentilis , n = 45). In 2023, WNV RNA positive birds were identified in only six federal states, as opposed to 13 federal states in 2024. All WNV RNA positive bird samples from 2023 to 2024 belonged to WNV Lineage 2 (WNV-2). Of the 86 sequenced samples, ~ 73% clustered within subcluster 2.5.3.4.3c. This subcluster, which also includes closely related sequences from Austria, Czech Republic and Slovakia, represents the dominant circulating variant. The remaining sequences (~ 27%) grouped within cluster 2.5.3.2, demonstrating the co-circulation of at least two genetically distinct WNV-2 variants in Germany. Conclusions These findings highlight the ongoing geographic expansion and local establishment of WNV-2 seven years after the initial detection of this virus in Germany, characterized by continuous virus evolution and the predominance of subcluster 2.5.3.4.3c, which suggests regional connectivity of transmission chains, underscoring the importance of transboundary surveillance and coordinated control measures.
Schwarzer et al. (Thu,) studied this question.